My thought was that it's a SetCursor() related issue, perhaps FRED specific (something MFC related) or maybe some regular OpenGL cursor setting bug. I'm not sure of when this started though so it's a bit hard for me to guess if it's a general OpenGL code thing or not. If so then it would have to have been an issue for most of this year, but not last year (sicne my changes are newer than that).
If SetCursor() has a NULL value passed to it then the cursor will disappear, and it's possible that it just isn't getting turned back on. I think that there is an OnSetCursor MFC call in fredview.cpp somewhere (there should be anyway) so a trace through that, and maybe a little playing around for the sake of testing, may turn something up. It may just rule something out, but it's worth a look anyway. That's where I was going to start back in my search for this problem.