What are you using as a reference plane? The open door is not necessarily perpendicular to the film plane I wouldn't trust it. A ruler across the open back may be more reliable, this might allow comparison of distances between the standard and the film plane, if the top and bottom measurements don't match there may be a problem.
Most of these cameras operate at small apertures like f5.6 and smaller and the depth of focus at the film plane may not be so critical as it is on cameras that operate at f2.
When the bellows is in place it exerts some slight force against the standard, if there is "give" in the standard then the alignment with bellows in place may be different from without bellows.