Which OS should I chose?

Hi, I have a big problem, please give me some help.
I have a PCI card which read 16KB data from FIFO to the memory when an
interrupt came out.And the interrupt is very fast, almost 16ms a time.
I have written a driver based on windows for the card, but lost too
many datas.

I want to change a embedded system, which OS should I chose? Please
help me .thanks.