You can try saving the text flie that contains your log information under a different name (My Documents/Flight Simulator Files), delete the old one, in flight sim then start a new log, and finally change the name of the "old" log file to the name of the "new" log you have just created.  I did this about once a month for a while and got sick of it so I just made my own log on Excel.  It works out much better.

I don't know why it happens, but it does with me from time to time. What I  do is:
Open the FS9.cfg and search for the entry "LOG_FILE=" (without the quotation marks). Most likely you will see a strange string of characters behind it, instead of the name of your logbook. I do not know how they get there but they do. Delete them (but leave the "LOG_FILE=" in of course) and save the FS9.cfg Next time  the game wants to make an entry in the logbook it will open the default logbook.

Hope this helps
AJ