Hi Vishal,
[quote user="VIshal Talwar"]
there is enough of a delay between pausing and resuming that I miss the IRQ low signal.
[/quote]
What do you mean by a delay between pausing and resuming?
In this period (from pausing to resuming) there should not be any interrupts.
I think the issue is that you didn't really disabled the interrupt, otherwise how could it be (according to your scope capture) that interrupt arrived after pausing the SPI? (while IRQ Enabled? was low)
Yael