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TMS320F280033: TIMER0 interrupt not working properly

Samruddhi D
Prodigy 70 points

Part Number: TMS320F280033

Tool/software:

Hello,
              I have currently set up the interrupts highlighted in yellow in my project. I'm planning to use those highlighted with purple in future. Timer0 is configured to be triggered every 50µs. However, I have encountered a few problems with this.  

              I figured out the problem was with interrupt priorities since interrupt nesting had not been implemented previously. Attached screenshot is from section 3.5.5 (PIE channel mapping ) of the technical reference manual.

              I then referred this article to allow higher priority interrupts in both SCIA RX and TX ISRs, though user priority has not been set. I have observed that there are still some fluctuations (43.47µs – 54.46µs), which amounts to around 10% error. This GPIO is not used anywhere else in the code and the execution time for TIMER0 ISR is 11µs. When SCIA RX and TX interrupts were disabled and only EPWM4 and TIMER0 were running, the fluctuations observed were 47.96 µs - 52.02 µs. When only TIMER0 was running, the fluctuations observed were 48.07 µs - 52.02 µs.
What could be the possible issue?

Thanks, 
samruddhi D