Engine shakes severly, and almost no exeleration when car is warm, this only happens when altrntr is working.?

the engine shakes severely and the exeleration is next to none when the car is warmed up, but when i first start it and drive, it drives like a dream..but literaly after 3-4 mins, as soon as the car is warmed up, this dream turns into a night mare and it sputters and barley acceleration unless i really really stomp the pedal,, when rpm are high like 4.5+ its o.k but below that, its really really bad!! and the weird thing is..this ONLY happens when the alternator fuse is plugged in ( battery charging) without the fuse i could drive on forever...well...until the battery dies..please help!!?!?!