The same thing happened to my car for a period of time. It would do exactly what you are talking about. It did it for a couple of days and then stopped. I disconnected my battery for awhile and the problem has never returned. Whether or not that fixed anything I don't know. But it sure is annoying isn't it?
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White 1995 Mustang GT
Dynomax Cat-Back, Offroad H-pipe, K&N Filters w/o Air Silencer
My 1995 Mustang GT