This AM I did some additional tests, still trying to determine a rule set.
Trial 1 - Created a simple cube, shelled it out to a constant wall thickness, open at the top. single hole thru the bottom central to the part, single hole on the -Y face central to the face. Saved as STL, into Repetier. All faces show solid blue, Cura slicer produces a correct part with the holes thru.
Trial 2 - Part from trial 1, rotated 90 Deg in Z, side facing hole is now at -X. Out as STL, into Repetier. Repetier shows some faces in purple, quadrants in the hole as purple. Cura slicer fails to reproduce the bottom hole.
Trial 3 - Part from trial 1, rotated 90 Deg in Y, open face is now toward -Y, both holes are horizontal. Out as STL, into Repetier. Repetier shows some faces and hole parts in purple, Cura appears to slice correctly, reproduces part with both holes.
Trial 4- STL part from Trial 1, rotated, re-saved as STL. Repetier shows only minor streaks of purple in the bottom hole, all faces are blue. Cura fails to recognize the central bottom hole.
From all of this I deduce that any rotation of the part prior to STL export will produce a corrupted STL, This is a problem in my CAD system, not in Repetier or Cura. I have been accustomed to rotating parts to favor fabrication by the 3D printer. It would appear that I must orient the part in its original form when constructing it to avoid this problem. I am not fond of this solution but if it works, then so be it.
To your suggestion, I used the part from Trial 2 and anaylsed it. It shows that the part is manifold and normals are oriented. Nothing to "fix".
Question: Can Repetier rotate parts after STL import to orient them more favorably for printing?