the only legitimate reasons for the ok led to blink are either the ctrio is unconfigured or the plc is in pgm mode. since the ctrio will go back into run mode after a power-cycle, that tells me the ctrio's configuration (in rom) is still intact. which only leaves the option that the ctrio thinks the plc is in pgm mode.
the ctrio knows the plc's mode because the plc places a code in the ctrio's shared ram. for the ctrio to change to pgm mode, that value must be something other than the 'run mode' code.
so now the question is what's changing that shared ram value in the ctrio, or, (assuming the correct value is getting written to the module) what's preventing the ctrio from successfully reading and/or acting on that value.
but before we go any further, is the problem still present, and if so, is there any more information you can give me about it, or any more symptoms?