Email me an ips patch of the error-producing rom so that I can figure out what the problem is.
As for the chunk limit, it will probably not be reached. I reserved 3 more chunks in the rom for any overflow. The rom is generally divided into sections that are each 0x4000 bytes long, so I call each section a chunk.
Also, thanks for the replies. The feedback is helping make this editor more powerful and bug-free. Right now, I'm working on a new part that will let you edit the graphics. Unfortunately, since the graphics are compressed, they will shift around the rom when saved causing the addresses to shift as well. Many of these addresses are used in the cutscenes, so allowing some graphics to be edited causes the cutscenes to look messed up. Until I find where the graphics are edited in the cutscenes, many of the graphics including enemy sprites will be uneditable.
For now, only some of the graphics will be allowed to be edited. This includes the subtile sets that are unused in the second megabyte of the rom. In the editor, you can see these by accessing the second half of the primary and secondary subtiles. They look like the original graphics but changed slightly. You'll also be able to edit animated subtiles since those are uncompressed. All of Wario's graphics will also be editable since I've found where they are referenced in the rom.