Nice pastime, I like it, but reported resolving time is wrong. I'm used to play and resolve in some minutes and it reports times as 55 sec, 30 sec, even 13 sec. And honestly, I'm not so good :) Because it's written in Python, I do some investigations.

main.py - autosave method (def on line 701) ...this is called on a regular loop...
(btw why regular comment and not __doc__ format?)
   it calls save_game method

saver.py - save_game method (line 144) at the very first line calls jar_game method

and guilty is: jar_game method (def on line 48) on second line (line 50)
it calls timer.finish_timing method. 
If you need stop timer for preparing pickled pack (I doubt about it, can be pickled with timer running IMHO) and jar_game is called in loop, you must pause it and after work done resume it, not stop it for ever, IMHO. 

So after first regular call to autosave method timer is stopped. This explain these times < 60 secs, which is default autosave loop time.

remedy: comment or delete line 50 in saver.py (call to finish_timing meth)
(/usr/share/pyshared/gnome_sudoku/saver.py, you need root access or sudo rights on Ubuntu et similia). It works, probatum est.

Now I have times about 3+ minutes :(

Done with 2.28 version, but I downloaded latest fresh 2.29 sources and there jar_game calls finish_timing too.

Regards
Pietro