The 16-press thing makes it more likely a software but than anything else. Is this happening consistently only with this board and never with another?
Is this a PC-based setup? How is the IOIO powered? How do the precompiled examples behave?
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Does this IOIO have the same firmware as the rest of them?
Can you upgrade to the latest before we start digging to deep? What you're describing doesn't sound like a hardware issue.