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LPC2468 timer behavior - transition drom boot to application

Hello,
I wrote a bootloader that works just fine in doing IAP, jumping to application etc.
I do have one big problem though: the bootloader uses timer 1 to drive a LED. unless I disable that timer, the application usage of timer 1 is incorrect, namely: the IR flag is set only very long after the program is started by the bootloader. the processor clock settings are identical, and the bootloader only starts the timer, without any changes to its configuration. what can be going on here?

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