With WorldEdit installed, If you use the residences selection tool it will make wrong selections sometimes. (Remember to set worldedit selection tool to a one different than residences).
I think this is because setpos when WorldEdit installed is doing strange things setting min and max values.

Verified bug, we'll push out a fix with 2.6.4 for this.

Fixed!

I personally am running WorldEdit and Residence on the same server and never had any problems, and the worldedit tool is different from the one in Residence.

Could you provide your Residence, Bukkit, and WorldEdit version, aswell as your config.yml?
Which tools do you have set for each respective plugin (Residence and WorldEdit) for selection?

Thank you!