MacbookPro Won't Boot without Live USB-Key. Screwed up bootloader?
You can mount the EFI partition with diskutil mount /dev/disk0s1
It should be empty, save for some firmware files etc in the APPLE dir - it's not normally used for the bootloader, but does make use of applicable files there if it can find any - so it is indeed a good guess that there is something in there throwing it off. The reason it works when you start by booting externally is likely the clean ESP on your external USB.

You can have a look around, and if you wish, just nuke the entire contents - again it's not used for booting OS X and anything in there will be recreated as needed, on the Apple side anyways.