Are you saying that because one pin is tied up looking for a pulse that it ends up missing pulses on the other pin?
Not sure if it'll help any (probably won't since a PIC is single threaded and can only act on one input at any one time unless you record any pulses you get and post-process them to see if anything useful was present during the time you recorded any pulses), but if you check your manual, you might find something that'll help you limit the MAXIMUM time the PULSIN statement waits for a PULSE (quite a few hints in that statement right there).





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