Denis
I would suggest to leave the profiler turned off, then go into Controls/assignments within the game and set-up all your buttons on the stick from within the game, to change assignments within the game you just DBL left click on the command you want change then press the new button to assign the new key.
The profiler that comes with the stick is really un-necessary unless you are wanting different key combinations for different planes and things like that........which I dont think what you have in mind

I just went back and re-read your question and perhaps you have changed the rotary mode selector button on the front of the stick which could change the inputs you have programed, so just turn that dial and see if your functions come back .......I would still suggest you leave the profiler off and re-assign within the game....it is easier than using the software......hope that helps.
PS.
even if your not quite ready for the yoke, the pedals will make such a huge impact on the realism of your sim enjoyment, I use CH pedals not Saitek, but I'm pretty sure that all you need to do is plug them in and the main axis' should just automatically work with no........complications, or need to program.......just enjoy them 8-)