If your PDP is blinking red then you have a wiring/hardware issue. Re-imaging should not fix that. See PDP LED section in User' Guide for more info on LEDs.
Also when you power up the robot that only has PDP+RIO on CAN, the LEDs may be red for a few seconds (say ten seconds to be safe). RIO doesn't enable CAN immediately, meanwhile the PDP LEDs will blink red.
If re-imaging the RIO "fixed it" then it could be the issue documented in the 2-24-2015 team update. Are you using C++? If so then that makes sense, in which case you might want to update your wpilib plugins.
http://contentviewer.adobe.com/s/FIR...24.html#page_0
I'm glad you figured it out, I just don't want teams needlessly re-imaging their RIOs. It takes a while to re-image, and then you have to re-deploy code. If you have a doubt, it might be easier to un-deploy your code first, reboot, and try that. That accomplishes nearly the same result as re-imaging.