rMBP Keyboard and Trackpad stop working on wake

Upon waking up my rMBP the keyboard and trackpad were not responsive but the backlight came on. Prior to lifting the lid I had plugged in a HDMI connection to an external non-apple 27" monitor and a USB connection(needed to route the HDMI signal no mouse or keyboard) to the KVMP switch. I have use this configuration for the past month or two. I had Parallels 8 running with a Win 7 VM. I closed the lid and unplugged both usb and HDMI connection and tried it again, no luck.

I plugged in my magic mouse which did work and plugged in a USB keyboard to log in and shut everything down cleanly. Rebooting fixed but I'd like to know why this happened. If I was away from home, I wouldn't be able to grab a usb keyboard to log in or do anything. I also don't want to have to do a hard shutdown if I can avoid it.

Searching I found a few others with a similar issue but magic mouse or another keyboard didn't work.

I will try a SMC reset and hardware test if it happens again but is there anything else anyone has seen or heard of that may cause this issue?

15" rMBP Late 2012 512GB SSD , 16GB ram.