when you did the test did you lock the gibs on the stationary axis?

The other thing i would do is put the base of the engineers square in the vice but proud of the top and indicate along that in the X to make sure its still aligned that way - it should be. with the Y-gib locked. Then move to the other leg of the square, lock X and release y and then indicate Y. that way you haven't got any disassembly between tests... or do the same things with a 123 block on the 3+2 sides.

If the ways are not machined square I suppose it would be possible to have them recut and fit a wider gib-strip (if need be). You could remove the table then indicate the Y axis movement relative to a square clamped to the x-way... that would give a clue as to which way is mis-aligned