I tried that as well, but the problem remained.
It had to do with the save file, simply because it is the only variable that didn't change when I was testing.
Picking an old save file or starting a new one doesn't raise any issue.
Lastly, I don't think the glitch is linked to the ruins, but to the otherall mecanics of the game. The glitch occured in the Royal city for me and for some it was in diama's floating temple.