I see what you mean - what comes into my mind is
either you make REM unique by adding a char like semicolon,
hopefully this is allowed by the compiler, or you make sure that
REM is the only UPPERCASE version of the source code and disable
IgnoreCase option.
this reminds about an issue with config files.
As you uninstalled, did you delete APPDATA directory as well?
If you are using APPDATA configuration of course, maybe you wanna give it a try
to rename the %APPDATA%\notepad++ directory and then start npp.
What I’ve done before to avoid this issue is you can rename your plugin. For example the installer removes DSpellCheck.dll I’ve just renamed it to DSpellCheck2.dll and it never warns me about it again :)
I did a few tests with BOM files and it seems that now “Encode in UTF-8” does remove the BOM. This makes total sense but it turned the previous logic upside down.