Nope, I don't use a 'blad, but haven't noted any issues with alignment in the way you describe. A friend of mine does use one and also regularly uses Fomapan100 and I haven't heard problems from him in this regard.
However, he does run into problems with minute cracks in the emulsion that are argued by some to be caused by the tension a Hasselblad transport mechanism exerts on the film. The problem seems intermittent and does not occur only with his Hasselblad but also with his Horseman view camera and accompanying holder. I myself, mostly using a Bronica, have not experienced this particular issue.