I did the same thing -- saved a copy of the prior INI file and used v28 for v29 (I always do this).
Yes, both started on the same 5K monitor. I have three 5K guys: left, center, and right. All tests are on the center (main). Check this out after running these lines:
echo Primary: %@winmetrics[0]x%@winmetrics[1]
echo Virtual: %@winmetrics[78]x%@winmetrics[79]
echo Monitors: %@winmetrics[80]
v28 reports the Windows scaled sizes, v29 reports the full screen sizes. How can this be?
It occurred to me that TCMD or TCC had to have a DPI override. Sure enough, the v29 TCC.EXE had the "High DPI scaling override" checked to use "Application". How? I have no idea. I'm the one and only user and I certainly did not do this.
Now that it is off, v29 reports the proper 2560x1440 and does the right thing with popup windows. When running the app noted previously -- it now scales all elements properly. Now I'm back to the original problem that started this thread: some of the toolbar icons in v29 are small, where others are the proper large size.