>>>Anyway, the code for the ISR is big,
>>
>> That is always a bad sign ...
>>
>
>This is not a true statement. I have several times developed
>systems that required accurate timing for complex functions
>( multiple simultaneous software UARTs, software video
>generation) in which nearly all CPU time, and a large proportion
>of code were in a (timer) interrupt handler. One useful trick
>here is that you may be able compute the correct outputs for
>interrupt N+1 during interrupt N, save them, and them output
>them at the very start of interrupt N+1. This can result in
>(on a PIC at least!) ZERO jitter.

Granted there are specialised cases where one puts a lot of code in the 
interrupt, but these cases are really 'the exception that proves the rule'. 
You NEED to know just what you are doing to make it work right, and take 
some care about how it is coded.

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