i would do one of 3 things, depends on if you have stuff you need to save on it, and how far your willing to go. i would recommend using the recovery menu to restore the ps3 to default settings and format the hdd while your at it, that way you can eliminate software problems completely.
the second option is try and downgrade to 3.41 and use the older drive pairing tool and see if that works, however the final option is one i do with every console i repair and that is trim a tiny bit off the end of the ribbon cable attaching the bluray to the ps3 as i have had lots of problems traced back to faulty or worn clips, mostly on the main board end.
if you do do this be very sparing - not much needs to be taken off and once the ribbon is in don't remove it again, as it could happen again. try the easy stuff first as software can be replaced/backed up.