MacbookPro Won't Boot without Live USB-Key. Screwed up bootloader? Following a Hard-drive crash, i replaced the Toshiba original HDD With a brand new Seagate ST500LT012-1DG142 Media Hard Drive. 

The OS X Mountain Lion installation went fine, however i'm stuck at the white screen durring boot. after a few minutes the question-marked folder shows up. 

The workaround i've found is booting with a Ubuntu live USB key. In that case, the HDD is seen in ubuntu, i can browse it just fine, and if i reboot after opening a session in Ubuntu, MacOs Boots up normally.. oO 
So i assume it's not a hardware problem. Partitions seems to be okay as well, diskutil list output : 

/dev/disk0
#:                       TYPE NAME                    SIZE IDENTIFIER
0:      GUID_partition_scheme                        *500.1 GB   disk0
1:                        EFI                         209.7 MB   disk0s1
2:                  Apple_HFS Macintosh HD            499.2 GB   disk0s2
3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3


Any ideas? Is there any way to check the EFI Partiton? OS X works fine in itself, and i'd appreciate to avoid a re-install, as my bandwith is not so good it takes a lot of time...
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.