... However, I think that the software wrongly thinks that at 11...Bf2+ the position is not equal to that of 13...Bf2+ and 15...Bf2+, because white had the right to castle prior to the first check. What do you think?
I believe you hit upon the reason. Not only does the position have to be repeated three times but all possible moves from the first position have to be possible in the third and that includes the right to castle. Technically white didn't really have the right to castle, since you can't castle out of check, and this might be an edge case.
I'm 99% positive that the chess.com triple repetition draw code just looks at the FEN string of the positions and the FEN for the first position would not match the second two, due to the ability to castle in the first one, since that isn't removed from the FEN until after the King (or either rook) moves..
Edit: Solved
While playing the Computer4-Impossible I encountered an abnormality as I was claiming a draw by the threefold repetition rule.
The game can be seen here:
http://www.chess.com/blog/pHUMpK1Ns/my-first-half-point-vs-computer4-impossible
With white I claimed a draw after 15...Bf2+ and I expected the game to end instantly, but the draw was first given after I moved 16.Kd2. At 15....Bf2+ the position on the board has been repeated 3 times with the same colour to move. However, I think that the software wrongly thinks that at 11...Bf2+ the position is not equal to that of 13...Bf2+ and 15...Bf2+, because white had the right to castle prior to the first check. What do you think?