I have an application that is using a timer in periodic mode. It fires at 100ms most of the time. However, in a 24 hr period I get around 35 occurances where it seems like I get a missed pulse and then two pulses back to back (I used a scope with a digital output to log this). My process executes for around 40ms and is the only thing running on the system. I have increased the priority to 40 and set the system clock to 100us to see if this helps but it just reduces the jitter.
Cheers.