Dimensioning an isometric view can be problematic, and I rarely do it. When I do I usually try to select parallel edges to dimension instead of a single edge. I can't tell by your screenshot if that would be possible, but it's something to look at.
Glenn Schroeder is spot on ... It all depends on which edges you select. Sometimes it fixes itself, but it's wonky ... (If that counts as a legit word, haha)
With outer edges selected ...
With the edge itself selected ...
I have already added small lines (which you can hide, by adding them to a layer etc), then dimensioning from those lines. Did you try points instead of lines??