In case it helps, here is some info from my experience, in which draggable overlays work fine. I use the separate windows option.
VASSAL 3.2.17, VASL 6.3.3
macOS Sierra 10.12.3
Java 8 update 121
Log:
2017-01-27 10:00:22,854 [0-main] INFO VASSAL.launch.StartUp - Starting
2017-01-27 10:00:22,857 [0-main] INFO VASSAL.launch.StartUp - OS Mac OS X 10.12.3
2017-01-27 10:00:22,857 [0-main] INFO VASSAL.launch.StartUp - Java version 1.8.0_121
2017-01-27 10:00:22,857 [0-main] INFO VASSAL.launch.StartUp - VASSAL version 3.2.17
2017-01-27 10:00:23,141 [0-AWT-EventQueue-0] INFO VASSAL.launch.ModuleManager - Manager
2017-01-27 10:00:30,539 [0-SwingWorker-pool-1562060294-thread-1] INFO VASSAL.launch.AbstractLaunchAction - Loading module file /Users/dmu/Dropbox/DB_VASL/vasl-6.3.3.vmod
2017-01-27 10:00:31,415 [0-SwingWorker-pool-1562060294-thread-1] INFO VASSAL.launch.TilingHandler - No images to tile.
2017-01-27 10:00:31,417 [0-SwingWorker-pool-1562060294-thread-1] INFO VASSAL.launch.AbstractLaunchAction - Loading module VASL
2017-01-27 10:00:31,425 [0-SwingWorker-pool-1562060294-thread-1] INFO VASSAL.tools.io.ProcessLauncher - launching /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java -Xms512M -Xmx1024M -DVASSAL.id=1 -DVASSAL.port=51128 -Duser.home=/Users/dmu -Duser.dir=/Users/dmu/Dropbox/DB_VASL/VASSAL.app -cp Contents/Resources/Java/Vengine.jar -Xdock:name=VASL -Xdock:icon=/Users/dmu/Dropbox/DB_VASL/VASSAL.app/Contents/Resources/VASSAL.icns -Dapple.awt.graphics.UseQuartz=false VASSAL.launch.Player --load -- /Users/dmu/Dropbox/DB_VASL/vasl-6.3.3.vmod
2017-01-27 10:00:32,025 [1-main] INFO VASSAL.launch.StartUp - Starting
2017-01-27 10:00:32,034 [1-main] INFO VASSAL.launch.StartUp - OS Mac OS X 10.12.3
2017-01-27 10:00:32,034 [1-main] INFO VASSAL.launch.StartUp - Java version 1.8.0_121
2017-01-27 10:00:32,034 [1-main] INFO VASSAL.launch.StartUp - VASSAL version 3.2.17
2017-01-27 10:00:32,034 [1-main] INFO VASSAL.launch.Launcher - Player
2017-01-27 10:00:34,349 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - VASSAL images folder found at jar:file:/Users/dmu/Dropbox/DB_VASL/VASSAL.app/Contents/Resources/Java/Vengine.jar!/images/
2017-01-27 10:00:34,353 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family network-server created for network-server.png
2017-01-27 10:00:34,353 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family go-down created for go-down.png
2017-01-27 10:00:34,353 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family network-idle created for network-idle.png
2017-01-27 10:00:34,353 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family VASSAL created for VASSAL.png
2017-01-27 10:00:34,353 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family calculator created for calculator.png
2017-01-27 10:00:34,353 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family go-up created for go-up.png
2017-01-27 10:00:34,354 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family VASSAL-jabber created for VASSAL-jabber.png
2017-01-27 10:00:34,354 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family jabber created for jabber.png
2017-01-27 10:00:34,354 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family bug created for bug.png
2017-01-27 10:00:34,354 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family yes created for yes.svg
2017-01-27 10:00:34,354 [1-IconFactory-preload] INFO VASSAL.tools.icon.IconFactory - Icon family no created for no.svg
2017-01-27 10:00:35,734 [1-AWT-EventQueue-0] ERROR VASSAL.i18n.BundleHelper - No Translation: Icon when pieces and draggable overlays are showing:
2017-01-27 10:00:35,734 [1-AWT-EventQueue-0] ERROR VASSAL.i18n.BundleHelper - No Translation: Icon when only draggable overlays are showing:
2017-01-27 10:00:35,734 [1-AWT-EventQueue-0] ERROR VASSAL.i18n.BundleHelper - No Translation: Icon when only map is showing:
2017-01-27 10:00:36,894 [1-AWT-EventQueue-0] WARN VASSAL.launch.BasicModule - VASL version 6.3.3
2017-01-27 10:00:36,941 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/3d6.mdx
2017-01-27 10:00:36,950 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension 3d6 v1.0 loaded
2017-01-27 10:00:36,951 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/5FB.mdx
2017-01-27 10:00:36,978 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension 5FB v5.6 loaded
2017-01-27 10:00:36,978 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/5KIA.mdx
2017-01-27 10:00:36,987 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension 5KIA v5.7 loaded
2017-01-27 10:00:36,987 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/Aircraft52.mdx
2017-01-27 10:00:37,015 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension Aircraft52 v5.0 loaded
2017-01-27 10:00:37,015 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/BFP_v403.vmdx
2017-01-27 10:00:37,078 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension BFP_v403 v4.03 loaded
2017-01-27 10:00:37,079 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/ChapterD.mdx
2017-01-27 10:00:37,083 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension ChapterD v1.0 loaded
2017-01-27 10:00:37,083 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/cloaking-display.vmdx
2017-01-27 10:00:37,099 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension cloaking-display v0.0 loaded
2017-01-27 10:00:37,099 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/Drag-over-ext1.mdx
2017-01-27 10:00:37,102 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension Drag-over-ext1 v0.0 loaded
2017-01-27 10:00:37,103 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/festung-budapest-1.2.vmdx
2017-01-27 10:00:37,144 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension festung-budapest-1.2 v1.2 - 8 May 2014 loaded
2017-01-27 10:00:37,144 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/MapInv.mdx
2017-01-27 10:00:37,164 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension MapInv v0.0 loaded
2017-01-27 10:00:37,164 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/secret-dr-1.0.vmdx
2017-01-27 10:00:37,172 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension secret-dr-1.0 v1.0 loaded
2017-01-27 10:00:37,172 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/SniperFinder.mdx
2017-01-27 10:00:37,194 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension SniperFinder v1.0 loaded
2017-01-27 10:00:37,195 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/terrain-chart-1.2.1.vmdx
2017-01-27 10:00:37,198 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension terrain-chart-1.2.1 v1.2.1 loaded
2017-01-27 10:00:37,198 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Loading extension /Users/dmu/Dropbox/DB_VASL/Extensions/VBM.mdx
2017-01-27 10:00:37,204 [1-AWT-EventQueue-0] INFO VASSAL.build.module.ExtensionsLoader - Extension VBM v5.7 loaded
2017-01-27 10:00:47,032 [1-AWT-EventQueue-0] INFO VASSAL.launch.TilingHandler - No images to tile.