Ok guys I think I figured it out.
Seems this issue was related with msvcrt linking on Debug mode.
The fread call was located inside a library linked against msvcrtd.lib while the executable from where the error was raised was linked against msvcrt.
I'm kind of surprised this was only causing issues with fread. Are the libc symbols located inside msvcrt under Windows ?
Anyway, I'm currently cleaning my link flags. Sorry not to have been able to post a more detailed code sample. We are working under very strict NDAs and I did not excpect this to be related to the link flags ^^'