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TMS320DM8148: Wrong readings from capture register

Part Number: TMS320DM8148

From time to time I get wrong values from the capture register or get different readings while the capture register isn't enabled.
The setup is as follows:
Timer4 is connected to an external clock (FGPA) and the timer is configured to run in 100Mhz.
TCAR1 input pin is connected to an FGPA.
The FGPA triggers a capture event, and also triggers an interrupt which is handled by the DSP. This happens every 250us.
In the IRQ handler I read the value of TCAR1 several times and then enable the next capture (set TCAR_IT_FLAG).

I expect the values to be the same in every read but every once in while I get different readings between the first and second readings, or between the first two readings and those following them. In rare cases, I read a value which is a little smaller than the one in the previous IRQ (as if the timer went backwards since the previous capture).
For debug purposes, I also added a verification that there's an event pending before reading the capture register (TCAR_IT_FLAG == 1).

Thank you