In junction with BetterShop I have been using LocalShops for player owned shops, and recently the two starting conflicting, LocalShops taking all the /shop commands instead of it going to bettershop.
After asking the devs for LocalShops about it they said that it's on your end.
http://forums.bukkit.org/threads/econ-localshops-v3-1-0-fifth-avenue-economy-based-player-shops-766.17131/page-6#post-318969
Apparently you are using command aliases incorrectly and this causes conflicts.
Please fix this!
While my global shop is much more important than the local shops, I can't with a good-mind drop a perfectly well programmed plugin simply because the other plugin does something wrong.