This problem has been reported for a while and as far as I can tell, I can't seem to find any code that would change the hideflags of the file whatsoever, so I thought the script to manually change the hideflags would solve it for good... Hm... maybe because the file is an icon to a script, that script could be having a hideflag applied to it and that's passed on to the icon somehow...? I do have some code within STM that changes the hideflags of the meshfilter and meshrenderer components, but I can't see how it's related to the icon... I'll be able to take another close look at this soon, sorry for the delays. But this really is a strange problem that's been bigger than it has any right to be. This is very good information though, if it's something happening just during editor runtime, that narrows down where the problem is.
If you want to test something for me, within the file "SuperTextMesh.cs" there's a method named "HideInspectorStuff". if you remove everything within that method, does the problem still occur? This is the part of the code that sets the meshfilter and meshrenderer hideflags I mentioned. I haven't been able to reproduce the bug in a while so that would be a huge help!