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On each DAT update VSE flushes its cache and start sacnning all accessed files. In your case what I will suggest you to see Access protection log of machine in question and note the processess which are blocked and the rule which is blocking them, make a list and then apply the exclusion on that single machine.
I belive this would really increase performance and application issue as well and later on you may apply the exclusions on all machines.
Further you can also set Low and high process policies as well. and put your application's process in low risk. Inthis way they will be scanned but with trusted level and this would not breach your company policy and obviously performance will be improved.
Go get the McAfee Profiler.
Users are trained to assume security is always at fault. It will take time to educate them that 95% of the time, that isn't the case.
I know its been a while but Id like to thank both of you, Alex's method helped with another issue and the profiler has helped me with two other people already. The original person though hasnt gotten back to me because they believe they are "having trouble getting it to read correctly". Which I honestly think is because Mcafee isnt causing the issue within their ancient applications and he cant get the profiler to indicate that. I could be wrong though.
But really this profiler will be extremely useful going forward, and the process for creating exceptions and setting priorities helps when/if we do have to create the exception.