Do you have track detection enabled so that it automatically attempts to split out each track? (I'm assuming that's the case.)
No I don't use track detection, Didn't care for it.
Not being shy about doing my own track splitting, I always record the entire side of an album at one time, then I manually split out the tracks. I also then name the files manually, but that's just my preference.
I do the same as you except I use Music ID to get some of the songs labeled then finish the rest.
The song just disappears.