Royaken's Song Hack Releases!

I'm not sure what to tell you other than it has to be the fact that you aren't removing headers from both ROMs or there is something with the programs you are using? You should always make sure to have both files start out either with or without headers so the IPS creation program can accurately make the data compare before creating the IPS file. The second file must only contain the different data.

If you are still getting large IPS file sizes I would recommend re-downloading Lunar IPS and try another hex editor? I used Hex Workshop 3.1 to delete the header, expand the ROM, and import the data over then used Lunar IPS version 1.02 to create the IPS I linked above.

I personally would never use a "tool" to remove a header, I've always used a hex editor and simply select then delete the 512 bytes ($200) manually. Makes the process much easier and fool-proof. :)