I was getting the below error message when I started up Protege_3.5
"Windows error 2 occured while loading the Java VM"
The root cause appears that in Protege there is a file called "Protege.lax" which contains the properties by which Protege launches and uses Java. In it there is the following part:
# LAX.NL.CURRENT.VM
# -----------------
# the VM to use for the next launch
lax.nl.current.vm=C:\\Program Files\\Java\\jre1.8.0_60\\bin\\java.exe
and as you can see from the last line it points to the install path of Java with the version. Apparently I had forgotten that I had installed a different version since then, which was causes the error. A simple edit to the correct version on that line enabled it to start up properly