My understanding is that Windows is non-deterministic and can be trouble when using it for data acquisition. Using a 32bit bus, and dual core, is it possible to use inline asm to work with interrupts in Visual Studio 2005 or at least set some kind of flags to be consistent in time with little jitter?
Going the direction of an RTOS(real time operating system): Windows CE with programming in kernel mode may get too expensive for us.