MIDI import was overhauled in 3.1, to support merging multiple MIDI documents into the song (remember the tedious copy-paste between instances?)
But it doesn’t support drag-drop in a selected track - new patterns are always appended to the song (it could appear to work that way the first time, but that’s only because you’re loading into an empty song?)
You also have some MIDI import options which can be configured by rightclicking a MIDI file from the Disk Browser (Load with options).