I've had the same problem before on similar 3x9 drivetrain.

It defies (my) logic why 7 of 9 (ooh ...jerry) gears shift good and #5 and 6 are trouble. This has happened to me a couple times after rebuilding drivetrain with all new parts. Eventually it went away after 50-100 miles. I'd adjust the cable tension a click or two during this process. One of those problems that seems to fix itself. Seems like the middle gears are always a bit hit-or-miss on one of my bikes - its running a 105/12-25 cassette.

So, i don't know why this happens, but I know that it does. My opinion is that some cassette gear combos just dont shift as good as others, and that your problem lies in your choice of cassette. Try swapping the cassettes on your bikes for a short time - just as a quick and easy test.

You might try posing this question on the mechanics forum to Sheldon Brown - he may know. If you find out what causes it, please let me know as I'm curious as to the root cause.