Have Asrock possibly printed wrong labels on the memory slots (confused the numbering)? Which ones are supposed to be populated first according to the user manual? If you have a chance, borow two more DDR3 strips from a friend and populate all slots. See what happens. If the RAM is then fully recognized and the system boots - it would confirm my idea above... If not, well, that would be a hint that the A-group of slots may be faulty. In that case I'd rma the board. Or check if there is a BIOS update that might sort the problem.
Was the CPU cooler really completely down on all four mounting points? Unless the CPU itself was not properly lined up inside the socket I can only imagine unevenly applied pressure to be a reason for that...
Coming to the thermal compound - I'd strongly recommend to be very careful about not redoing it. At least do yourself a favour and thoroughly stress-test while you're closely monitoring the temperature
Anyway, glad to see that you were able to sort it out by an easy and inexpensive solution.