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You could always try excluding the java extensions from the script scanner component of VSE and see if it makes a difference, or exclude them from the on-access scanner. Not that I'd recommend that you do that indefinitely but it will let you know which component is still scanning the files, if any, and then you can take it from there.
Hope it helps,
thanks for your help Gary,
I have already disabled script scan and added all the folder exclusions of their development tools to the on-access scanner. It seems to help for a few weeks then everything started getting slow again.
These users have never had an virus issue so im prepared to be a bit lax with their security if it improves their productivity.
Currently evulating if safeboot 5.2.5 could be causing the slowness, the machines have over 1 million local files (one has 2.5 million....) and trying to remove safeboot is going to take 16 hours....