Aren't you approaching this from the wrong perspective?
If you turn off the accessibility options how are users with disabilities going to be able to use the computers?
Shouldn't you be doing quick cards to put by the machines that guide users how to temporarily turn off the options while they're using software where the accessibility options clash?
And thinking longer term - you didn't really say what this software was but off the top of my head I'm struggling to see what the educational value is of a piece of software that requires users to press the same key many times in a row
- unless it's some psychometric test to see how quickly they get bored with repetitive pointless tasks
I don't know what country you're in, but from a legal point of view have you considered whether or not you're breaking disability discrimination laws by having software that apparently can't be used by students with disabilities?
Apologies for opening up a can of worms for you