First of all, I should mention that the built-in music playback tool in the NESmaker UI is not very accurate to what you'll hear in-game. It doesn't observe pitch or arpeggio envelopes, and the volume mixing is very off.
The reason why your music sounds slower in-game than in FamiTracker is because Mesen is running the ROM at PAL speed with NTSC designed music. That's just something you can fix in Mesen's Region settings.
The weird off-sounding note you hear in the actual ROM is because GGsound does not recognize notes below A-0. In FamiTracker, any note below A-0 sounds identical, but GGsound can give you some really odd pitches when using them.
Also I should mention, GGsound does not recognize anything written to the note effects column or the channel volume column (with the exception of Bxx when using GGsound's official ft_txt_to_asm Python script, and even that has caveats). Anything written there will be ignored in the compiling process.
I'd highly suggest you read over this guide to creating NESmaker-compatible music and SFX with FamiTracker: https://www.nesmakers.com/viewtopic.php?f=39&t=3018