Java issues.

I hope this is the right thread. Please bare with me as I am desperately searching for the answer to my question. I work with an IT firm and I'm trying to solve an issue. We have been noticing lately more an more problems with an internet based application we use. It based an ran off Java, then works with a program we used called RAFT. I've noticed people are having problems with this internet based application more frequesntly when the "keep temporary files" is unchecked vs checked in Java setting on My Computer.

My question I'm asking is, will java files create issues if temporary files aren't enabled? This are mostly blank page issues that happen where the app doesn't load correctly or the app has greyed out areas in certain spots on the page.
Like i said these people usually only have this problem frequently, (like weekly, sometimes daily). VS . The other people that have this issue.

I guess the two questions im really asking are
1. Why are temorary java files good
2. Would they cause this issue.

If I could get support on this team i'd appreciate it! Seriously! If you would ask any colleagues/Coworkers/Friends to help give me a good idea id mean it.

Maybe even a little 101 on java too..

Thank you so much!