The way I determined it, the bugs about PNG saving, misplaced Thing placeholders, black layers (thanks, DW!), etc. actually all have to do with major bugs dealing with SRB2 graphics not being available. Basically, if you don't rip SRB2 graphics to PNG for this program's use, the program is as good as not working. This has been fixed.
I believe I can also deal with the bug of Maptosvg simply not running on some peoples' machines. I believe this has to do with the framework (PHP, PHP-GTK2, and GTK+) builds. They've been swapped for Beta 2.1 v0.51 using builds in which I have more confidence in.
Actually, Beta 2.1 v0.51 -- a major bugfix release -- is more or less complete. PNG saving should work without qualms now and the program should work a lot better when SRB2 graphics aren't available. The only thing is that I discovered a new method I can use to save to PNG (and even preview the map within the program!) I can't get it to work right now, though, so I'm waiting for a support forum to get back to me, if they will. :)
(DW: Are you using a more current version of your map? Send me a PM. I find the ongoing issue behind your map pretty interesting.)