Look in fs9.cfg for the line "log_file=logbook", even if it reads correctly overwrite it with that data (minus quotation marks).  Now open logbook.log and look for anything amiss (duplicate data stuck out to the right of normal listings is common, as is missing AC type), correct anything you can, delete any lines you're not sure of;  at most you may lose a few flights.  You should now be able to access the logbook in the sim again.  If all is well, it's a good idea to backup logbook.log (I just right click > "add to zip"), logbook corruption is not uncommon.

In Vista, FS9.cfg is in ...users\"name"\application data\microsoft\fs9\

logbook.log is in ...users\"name"\documents\flight simulator files\

I have now re-checked the FS9.cfg file and the logbook.log file.      All seems to be correct.      In fact, if I enter a flight manually, it comes up in the logbook.log file correctly.      The problem seems to be that the system is not logging flight time automatically although the 'Log Flight Time' box is checked in 'settings'.