With MiniGL 2.20 and early version (2.5) I have found some problems with PrBoom Plus (in OpenGL mode only)
See this grab:
http://s000.tinyupload.com/index.php?file_id=16072589085825220168
As you can see actually we still have a rendering issues with the sky (but we still have also various problem with the trasparence effects)
As a test i even try the original PrBoom freely availible on OS4Depot and in that version there is no problem with the trasparence but for sure there is a problem with the sky colours ...
BSzili are currently working updating MiniGL so i take the chance to talk with him directly, however without the possibilty to access to your source i doubt he can do somethings usefull about that problems
http://www.amigans.net/modules/xforum/viewtopic.php?forum=25&topic_id=70...
Good news, BSzili fixed the trasparence issue directly in MiniGL library (see MiniGL repository) however sadly he wasn't able to do mutch for the sky colours issue that for now still the only issue remained
See here for details: http://www.amigans.net/modules/xforum/viewtopic.php?post_id=98553#forump...
Will those fixes come as some official MiniGL update (e.g. via AmiUpdate)
P.S. Is http://os4depot.net/index.php?function=showfile&file=utility/filetool/gr... Grunch better then amiupdate?