Sorry for the late reply. This is one of the things where I have to sit down and investigate, and I have limited time through the week. (And I'm sad to say, I probably would have forgotten about your post if it wasn't for your PM. I'll try to do better.)
Fixed in version 4.1.0.51. However, when building the mod, you'll need to use version 4.1.0.37 (or was it 4.1.0.36? It's been a while). Later versions have a problem when building ROMs that I haven't had time to fix yet, as it requires fixing nearly all of the dependencies. Believe it or not, one of the many things that needs to be updated is the save editor. I've been waiting for the save editor to be perfect before releasing it, but in all honesty, it's probably good enough for what the ROM editor needs it for. I have no ETA for when I can move forward and fix it, but I do plan to.
I've had a similar problem when there's a syntax error with my edits. There's currently no real error checking when compiling scripts, so try compiling the script manually to see if Lua gives any errors. The Lua compiler can be found at SkyEditor.ROMEditor.Windows/lua/luac5.1.exe in the zip file. Try using command prompt to launch luac.exe -o <output> <script>, where <script> is the script you're editing, and <output> is some temporary path to save the script. Don't forget to put paths in quotation marks if they contain spaces.