I just checked. The problem is the way the new line is encoded in the ini file. If it is linux style (known as LF, which is one byte), the tool truncates what comes after "enabled", this because it assumes Windows style new line instead (known as CRLF, which is two bytes instead).
If you want to replicate the bug, just open the ini with visual studio code, and at the bottom right select LF instead of CRLF, and save.
I believe Hekate creates the emummc.ini file using LF new lines, then your tool cannot be used after creating emuMMC with Hekate, unless you manually fix it first. This might prevent many users on using your tool in the first place.