Just to add my experience to what seems to be the same problem. I've got an weather app running 24/7 that uses just about all the different I/Os available. I too get a hung PulseIn.frequency. It used to work but now pretty much it will hang every few days. I use 3 PulseIn at a time calling them successively and it is always the third call that blocks. The signal is good on the scope and if I reconnect to the IOIO all works fine again. I can't be sure but it seems this started to happen with version 4. This is over BT but when the protocol gets corrupted the app usually just dies and the logs reflect it, so I don't think this is BT related. When it hangs everything else keeps on working, UART, TWI, PulseOut, digital I/O, and AnalogIn.
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