I ran into the exact same problem, as I also used to have all my logs in one folder. However, there is a way around it - select "Save by date" in the logging options and add a String registry key called LogsDateDirFormat under:
HKEY_CURRENT_USER\Software\Patchou\Messenger Plus! Live\<your_msn_address_here>\Preferences
...and leave it EMPTY - normally this key would contain a date format pattern by which Plus would create the folders (for a more detailed explanation go to
http://www.msgpluslive.net/help/registry ), but if it's empty, then there's no pattern and hence, no folders. Voilą!
