You don't need interrupts for counting pulses. Instead use the hardware 
counters inbuild in the AM335x CPU. Those are

   - 3xPWMSS.eQEP
   - 3xPWMSS.eCAP
   - 4xTIMERSS

Find details and example code (C, Python, BASIC) in the libpruio 
documentation 
<http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/>.

Regards

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