Weird things like that is part of the reason I never use the GUI for backups, restores and plenty of other things. There are other odd things like that it does since it's trying to make it easier for anyone to perform certain tasks for every possible combination of every scenario.
T-SQL should/did use the locations from the backup file - have no idea what the GUI does to change it around.You could always run a trace while you try to do the restore with the GUI and see what it is doing.

Sue