I remember reading (in another forum, I think) that it DOES support Chess 960, but there are bugs in the program. It's possible you found one of these bugs... and that this one is related to the analysis feature.
Can Fritz 13 Analyze Chess960?
Oh, okay. I guess that could be it. I'll keep experimenting and see if I can get it to go. 
I really wish Chessbase would get their own forums so issues like this could be better discussed. Never made sense to me to not have your own forums when you are a PC software company.
First of all, I don't have Fritz 13, and I don't have the answer to your question.
But here's how I'd go about it.
If the Fritz GUI isn't set up to specifically analyze in Chess960 mode (and I didn't see anything in the Fritz 13 manual that would indicate that capability), I'd first see if the Fritz 13 engine has an engine parameter for Chess960 mode. I'm not sure of the exact steps, but you'd have to go into the Engine menu and look at the engine parameters for the Fritz 13 engine to see if there's a setting for Chess960 mode. If there is, then enable that parameter and then try to analyze a Chess960 game with that engine.
If there isn't a Chess960 parameter for the Fritz 13 engine, then my next step would be to find a free UCI engine that has Chess960 capability (like recent Stockfish, Critter, and Spike engines). For example, you could install the Stockfish engine into the Fritz GUI as a UCI engine, making sure that you select the "UCI_Chess960" parameter during installation. (You could name the engine "Stockfish Chess960", or something similar.) Then try analyzing a Chess960 game using the Stockfish engine. If that idea doesn't work, then I'd punt. 
First of all, I don't have Fritz 13, and I don't have the answer to your question. But here's how I'd go about it.
If the Fritz GUI isn't set up to specifically analyze in Chess960 mode (and I didn't see anything in the Fritz 13 manual that would indicate that capability), I'd first see if the Fritz 13 engine has an engine parameter for Chess960 mode. I'm not sure of the exact steps, but you'd have to go into the Engine menu and look at the engine parameters for the Fritz 13 engine to see if there's a setting for Chess960 mode. If there is, then enable that parameter and then try to analyze a Chess960 game with that engine.
If there isn't a Chess960 parameter for the Fritz 13 engine, then my next step would be to find a free UCI engine that has Chess960 capability (like recent Stockfish, Critter, and Spike engines). For example, you could install the Stockfish engine into the Fritz GUI as a UCI engine, making sure that you select the "UCI_Chess960" parameter during installation. (You could name the engine "Stockfish Chess960", or something similar.) Then try analyzing a Chess960 game using the Stockfish engine. If that idea doesn't work, then I'd punt.
It's worth a shot! Thanks for the tips!
If the Fritz GUI isn't set up to specifically analyze in Chess960 mode (and I didn't see anything in the Fritz 13 manual that would indicate that capability), I'd first see if the Fritz 13 engine has an engine parameter for Chess960 mode. I'm not sure of the exact steps, but you'd have to go into the Engine menu and look at the engine parameters for the Fritz 13 engine to see if there's a setting for Chess960 mode. If there is, then enable that parameter and then try to analyze a Chess960 game with that engine.
You did it! That was exactly what I needed to do. Go into the Engine menu and select a special Fritz960 engine to be the "active engine". Now it is analyzing my 960 game just fine.
Thanks so much for the help! I didn't even realize that my copy of Fritz 13 came with six different engines (I don't recall that being the case with F11)!
Thanks again!
I just thought of one more possibility. Was the 960 game that you tried to analyze a game that you played in Fritz, or was it played on Chess.com? (There might be slight differences in the 960 pgn files created elsewhere.)
Edit - OK, I posted this before I saw your last post of success. Please ignore this post. 
I just thought of one more possibility. Was the 960 game that you tried to analyze a game that you played in Fritz, or was it played on Chess.com? (There might be slight differences in the 960 pgn files created elsewhere.)
Edit - OK, I posted this before I saw your last post of success. Please ignore this post.
Thanks for the suggestion anyway! It was a Chess.com PGN and I was curious if that was the problem, too. I tried different PGNs just to be sure and they didn't work either.
Thanks anyway! 
I recently upgraded to Fritz 13 and tried to get it to analyze a 960 game that I just concluded. Unfortunately, when I hit the "Full Analysis" button, nothing happens. Is Fritz 13 unable to analyze a 960 position? I could swear I used Fritz 11 to analyze 960 games all the time. ???