I have spoken with Autodesk and we resolved the issue, however without an explanation for what caused it. Somehow a reference plane became embedded in a floor definition (according to the support person it wasn't supposed to be that way). Anyway, when I suggested using the " view workplane" when we were exploring solutions, it showed the plane properly in the screen view, but when modifying the floor the edit mode was rotated. A little bizarre. With enough experimenting we were able to get the floor pattern corrected, but no real answer as to what caused the issue. The initial work around for those interested:
As the linked Revit model had the pattern oriented correctly, the support person selected the inserted link, then tabbed to the floor, selected it and hit copy, and then hit paste into the working project. Revit then inserted the floor as an object with the correct pattern orientation. Honestly, I didn't realize you could do that so easily, though it makes senses you could. The question we then spent about an hour working through was how the rotated pattern got that way as it never corrected even when selecting match properties between the rotated and correct floors. We did finally get it corrected as noted above, but without an understanding of what caused it.