Your LW preferences for LW 4.6 will be in a different location to 4.10 if you had to reset your preferences. AFAI can see anyway. It might be an idea to delete the LW prefs in the .limewire folder. ie:
delete your LW Preferences folder whilst LW is closed; instructions here: Point #2 & 3 in Fixes for Limewire (sample image included at bottom of page.) Step 2 to delete the preferences folder for LW 4.6 which sounds advisable. LW 4.10 may behave more consistently then. If you're running it off an external drive then it's going to be slow to read. This might be part of the reason for problems relating the preferences folder. Particularly if the drive is formatted differently. It may well be to do with permissions also. I believe if you had LW installed on your main drive as Only A Hobo suggested, then you wouldn't have these problems.

As far as an external drive for sharing .... I sometimes have a firewire drive for sharing. But if I start up LW with that external drive not turned on then LW forgets about those shares. Even if I turn the drive on & restart LW, LW seems to forget about it. (But only happens if I've opened LW whilst the drive was not turned on.)