Thanks for your reply Saltgrass!
I retried the Startup Repair, but it always says the same thing after not finding my Windows installation. It says that it can't repair automatically. When I look in the details of the problem I see:
(I'm translating the messages because my Windows is in French)
Event problem name: StartupRepairOffline
Problem signature 01: 0.0.0.0
Problem signature 02: 0.0.0.0
Problem signature 03: unknown
Problem signature 04: 0
Problem signature 05: unknown
Problem signature 06: 1
Problem signature 07: unknown
System version: 6.1.7600.2.0.0.256.1
Regional settings ID: 1036
So I tried the commands you proposed in the command prompt.
bootrec /fixmbr worked OK, but I got an error the /fixboot command (again, it's the approx. message):
The volume doesn't contain a known filesystem. Verify that all the necessary filesystem drivers
are loaded and that the volume is not altered.
So, I ran "chkdsk /F" on the c: (boot partition) and on the d: (normal Windows partition). Both were identified as NTFS and no error were found.
The problem remains the same: it boot straight to PC-BSD, without any boot manager.
Thanks for your help!