First, we don't support Basic interrupts on Atom/Nano modules as of Studio 2.0s release, only ASM interrupts via the ISRASM{} block are garunteed to continue to function. This thread is exactly why we stop supporting Basic interrupts.

Sorry. To use the hardware capture function on the Nano or Atom modules you should setup the PIC hardware directly. Then use an israsm{} interrupt handler, which I've documented in atleast a couple other posts, to process the value captured. Also as Alan said you should never do anything as long as a Serial command in an interrupt handler. This isn't a problem when using israsm since you can't use basic commands in an israsm handler.
