Revisiting this again.

Actually, my previously accepted answer was not what it ended up being.

When using the MCP23017, I noticed that the GPIOA / GPIOB registry is very undesireable to poll when OUTPUTS are changed; but rather it is very consistent on INPUT changes.

Instead of polling GPIOA/GPIOB for output status, I instead wrote to OLATA / OLATB which forces the chip to be in that state. I am not saying it will be 100% right, but it has lead me to far greater success. I hope this backtrack will help you in the future if needed.