You have these files from PC or N900's native one? If it is the second, then my suggestion was to replace N900's files with one from your PC, if you don't have there issue with permanent logging. Also I would reboot the phone after replacement is done.

Also it's possible to copy files in other direction (N900-->PC) and check if this issue will occur also on PC. Before coping files from one or another direction it's smart to store somewhere original files (backup).