Disabling other processes on nios

Hi,

With some help from this forum, I've managed to get my project working well. The fpga reads samples from an ADC and enables a flag when the buffer is full. The nios2 polls the edge capture register, then when it sees the flag it reads the data, writes it to SDRAM, resets the edge capture register and repeats until it has read as much data as it wants.

This seems to work perfectly, but every now and again it misses some samples from the ADC, all in one block. It's a block of about 20 samples in every 1200, not disastrous but enough to be a nuisance. I assume the processor is periodically doing something else, so my polling loop is too slow. Does anyone know what else the processor could be doing and how I could stop it? I've tried disabling interrupts with alt_irq_disable_all() to no avail. Any other ideas?

Thanks

Bert