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LPC2468 unexplained behavior when jumping to application from boot

Hello,
I am new to ths processor to this is a rather difficult situation...If my bootloader uses CPU peripheral T0 (not interrupting, just a free running timer), T0 must be stopped just prior to jumping to the application in order for the application code (that uses an interrupting T0) to get interrupted by the CPU, otherwise it won't. If I initialize USB in the bootloader, resetting the peripheral does not help; the application should be interrupted by T0 but is not! but If my bootloader jumps directly to the application all is well.
Do you have a clue?