Timer PreScaler Inconsistency

I noticed in the course of data acquisition (EVM5515 + ADS1298) the timer0 with prescaler value 512 ran slower than with prescaler value 2. The test program shows that the timer1 ran 55.5 s in 60 s determined by the timer0.

1) Is there any known issues with timer prescaling?

2) How can the system clock be tested?

3) Can TI publish timer prescaling test documentation?

Thanks,

Sukru