I noticed the same issue on Windows 10 -> CoolSoft MIDIMapper -> UM-ONE mk2 -> SC-55 mk2 in latest versions of Chocolate and Crispy when a new track starts, looping seems to be fine. PrBoom+ with SDL set as the MIDI player has next to no stuttering, but the music sounds muffled, which is why I suppose PortMidi is recommended for hardware - that has stuttering on track start as well.