Problem solved ! It had absolutely nothing to do with databases schema nor annotations.
In entity A, one of my personnal setter was forcing type in parameter :
public function setB(B $objB) { //... }
... and I forgot to use B's FQCN ! That's why it was using A's one.
Next time I won't declare FQCN in the annotation to oblige me to use it at the beginning of my class ! :)