What about the CAP modules in the PWMSS? Two header pins are available (P9_28 and P9_42, max. 50 MHz). It's supported by libpruio <http://beagleboard.org/project/libpruio/>, ie. check out the pwm_cap example <http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/_cha_examples.html#SubSecExaPwmCap> .
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