is it overboosting or spiking? ie: does it just keep boosting beyond what it should be set to, or does it hold at std boost but spike in some gears/rpm?
If it's just rising past the set boost level, your waste gate isn't opening like it should. It could be stuck, or the waste gate actuator could be forked or your vac/boost line running to the wastegate actuator could be perished or leaking.
so you removed the manual boost control and put the stock one back in the loop? If there's no boost controller, or your wategate actuator is not hooked up to the boost/vac lines at all, it won't open and the turbo will just boost as much as it physically can.