I've also been seeing issues with elevation. Changing a junction, or maybe the elevation of one segment attached to the junction, seems to drop elevation from all the segments in the junction. This appears to be true even if I select the unexpectedly modified segments -- the standard WME segment properties show blank elevation.
If I have a segment that has directional or reverse connection issues and fix it, after I save, it gets highlighted for elevation out of range, but it wasn't highlighted for that before. (I.e., when I select the segment, it only shows the reverse connection problem, it does not also show an elevation note.) This may simply be a symptom of the above -- until I changed the junction to eliminate the reverse connection, perhaps the segment had a properly assigned elevation, so there was no reason to show an elevation note. Once I saved, and the elevation was lost, then there was a reason to display the issue.
So I'm going to vote for there being a problem with WME killing elevation values right now, or a problem with JNF/toolbox doing it.