Well like I said earflier, I'm in vacation away from the game code so I could not verify with the actual game code, but after hearing a lot of complaint I decided to try and find out what was causing the bug since I never experienced it myself.
So I did some testing based on comments on this forum, and I was able to reproduce the bug twice using the exact same pattern.
Basically, the problem seems to be occuring when you put the PSP in Sleep mode while playing a level. So DO NOT USE THE SLEEP function of the PSP and the progression bug should not occure. (The sleep function is activated when you hit the power button only one time)
I'm going to verify what is going on when I get back to work next week but until then this should make it possible to play the game without fearing to lose progression.