Question if you use ISOGEN much. Whenever you have piping that visually overlaps in the default isometric view, ISOGEN gets finicky.

E.G. model a C shape in CAESAR in the +X, then -Y, then -X directions. Now rotate that model -45° in the Y. All three lines now visually overlap in the default isometric view.

In my case, I had several tap connections coming out on the vertical leg, which also visually overlapped.

When I ran ISOGEN, the top leg was drawn off at a completely off-kilter angle than the bottom leg.