VDK use NMI or fixed mode interrupt to count performance events, but NMI callbacks are removed from recent linux kernels, compiling with USE_NMI failed in kernel 2.6.21. Fixed mode interrtups can be masked, so the long path intr disabled code can't be measured.
Just wondering: what is the processor on which you are attempting to measure the time spent with interrupts disabled. Also, what is the OS version? If you want to share the vtqfagent log file, I encourage you to create an issue on the http://premier.intel.com for this purpose.