Version 1.6.6 Bugs back to 1.5.8

This is in an educational environment on Win7 64 bit. We updated from 1.5.8 to 1.6.6. Randomly Arduino will not load. The bug check file is
Exception in thread "main" java.lang.NullPointerException
at processing .app.Base.getSettingsFolder(Base.java:2076)
at processing .app.Base.getSettingsFile(Base.java:2095)
at processing .app.Base.getSettingsinit(Base.java:230)
at processing .app.Base.Main(Base.java:167)
I worked on this for a while and found not much help online. What I did find on my own is that the a few files in the C:\Program Files (x86)\Arduino\lib folder revert back to version 1.5.8. So says version.txt. The big offender is the PDE.jar file. The others are formatter.conf, keywords.txt, and preferences.txt.
Any help as to stopping this from happening would be appreciated. I am hesitant to update to another version. My fix before was running an uninstall then reinstalling.

Why not install the latest version (1.6.7)? And is you Java up to date (8u71)? (stupid java...)

Try to uninstall Arduino completely. Check if the progfiles\Arduino folder is indeed gone and then install 1.6.7 from scratch.

1.6.6 and 1.6.7 are both a mess, use 1.6.5r5 until they fix the latest versions.

You need to manually delete the Arduino15 folder inside app data (I don't have the exact path handy), I think, if you had 1.5.x installed on the system prior to 1.6.x - it doesn't clean up after itself.

I found 1.6.5 buggy (but I'm not sure if it was r5..) Use 1.6.4 most of the time but have 1.6.7 installed on another machine and it seems to work okay...

There seems to have been an increase in people with bizzare build issues that nobody knows the solution for in 1.6.6/1.6.7