Os X always forgets my preferences

The bug I have is that os X won't automatically save my preferences...
for example, an application that I have deleted will keep appearing as a "question mark" in the dock.
Or the preferences that I have assigned to a particular program will be lost after reboot.
I have recently updated to Snow Leopard, but I think I had that problem just before... I hoped that updating would solve the issue, and it seems not to be the solution...
Does anyone recognises the problem ? ... as it is quit hard to troubleshoot
Yours,
Flo

Hey Richard,
thanks for the tip... I also came to that conclusion... I wondered whether it was necessary to do a back up as a "disk image.".. and if that was the solution to avoid having to reinstall all my programs... or if I could simply drag and drop installed programs from the back-up disk... I suppose Time Machine is my tool for that...
Also, I came to the conclusion that if my preferences won't save, it could be because somehow I don't have the "read and right" permission to do so in the Preference folder... Indeed, I came to the conclusion that I have changed my computer's name (for using an internal network to connect my computer and the Ipad instead of my rather weak Wifi signal )... and that my computer now has this new network's name. (I might have confused myself in the process).
Not very solid knowledge, but I hope this might be useful for others...
Yours,

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