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Uninstallings seems way over the top.
Just closing it should solved all the issues it might cause (by default it minimises to a tray icon).
About the only way it could cause FPS issues if somehow got stuck in a infinite loop, tying up the CPU (cores). Was there any significant processor activity while it was running?
Could it be you just had the issues for a short time while minion was doingthe bulk of it's work?
How certain was the administrator it really was minion (finding a single buggy programm as cause of a problem is about 50% trial and error - I know it, am Admin myself).
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