I've created csk holes in a sheetmetal part using the Insert > Hole method and now the axis don't run through the centerline of the hole. How can this be? I must be looking at something wrong but I can't imagine what could cause this.
Turns out it's a build issue. I submitted the problem to tech support via the web as was suggested on this list. Viola, I uploaded the part with my case request and had an answer back in less than an hour. Turns out this is problem with build 2002430 of Pro/E 2001 (don't know if it occurs with earlier builds or was only a problem with this specific build).
I downloaded build 2003360 (that's another long sad story) and magically the axis are back inline with the holes.
Interesting follow up. Before installing the new build of Pro/E I created two datum planes using the through option and picking two of the skewed axis. As you might expect the datums were created at a 45 degree angle to the surface of the part. When I openned the part using the new build of Pro/E the axis are now inline with the holes but the datum planes are still at 45 degree angles.
Doing a regen doesn't change anything. It says part hasn't changed since last regen. But if you suppress the first datum the second datum then aligns correctly with the axis and unsuppress results in the first axis being oriented correctly.