id say check the mouse issue as mentioned, and also run a calibration on the controller, it is possible that the dead zone (center) is not correct upon connection (this can be from holding the stick when pluging it in, or the native center on the control has been lost over time).
I use a PS3 controller and the only time I have ever had issues has been mouse related, or hitting Walk "Z" on compact. Other than that I can't think of a time when my PS3 controller has had any issue (other than its overly sensitive R2/L2 buttons but nothing I can do about that and it is the easiest for macro access.)
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