I'm having the same problem here. I guess this new versions changes (from 5.35 ahead) are causing all those troubles (migrating to x64 and change java platform).
I tried to debug some problems, but it's something on source code. One interesting problem I had was with XC-8/xc-16 new versions with MpLAB. I dont know why I couldn't reconfigure my project, nor compile. Now I'm using MPLAB IDE v5.40 and XC8/16 version 2.10. The only problem is the simulator itself.