I ran into the same bug. I had a save before I'd activated the tonal locks, but reloading and completing the puzzle again still didn't open the doors. I found that if I left the ruins, fast traveled around a bit, sold some things, & went into a number of different buildings that when I returned it worked. Good luck!
Brute Force Solution to Tonal Bug:
1) Save game upon arrival to Tonal Lock puzzle
2) Turn Off XBox, wait a couple of minutes
3) Turn On XBox and "continue" with game. 4) Solve puzzle
I have noticed that when the Tonal Puzzle refuses to work, you won't hear a musical note when you hit one of the resonators. If you hear a musical tone, there is a good probability that the puzzle will work just fine. It is unknown why the puzzle sometimes plays musical notes and sometimes does not. Maybe it has to do with a runtime error that's difficult to debug. If this type of runtime error is to blame, it makes sense as to why you must turn off and then on the XBox.
WILL TURNING OFF THE PS3 WORK AS WELL???
Keep your fingers crossed
I've used fireballs to activate locks, got that glitch, reloaded and used lightnings - everything went the right way. Probably glitch is related to area damage
I can confirm the 'turn off xbox/turn back on' method works. Save just before hitting the tonals, turn off your console, turn back on, reload your save, and hit them in the correct order with whatever missiles (arrows, bolts, magic) you have. Door opened for me.
What do you think?