I did a little more looking. In the main Cloudlog logbook, FT4 contacts are misidentified as MFSK QSOs, as below.
If you click on the guy's call you get a QSO Details window, which correctly identifies the QSO as FT$, as follows.
Finally, if you click on Edit QSO you get the edit window, which shows the mode as FT4 with some symbol in front of it (an arrow??)
So, I'm guess in here, but Cloudlog is either uploading the Mode to LoTW as MFSK (not legitimate according to LoTW) or it's uploading FT4 with that symbol in front of it, which I suspects LoTW also rejects.
I don't understand why FT4 gets labeled at MFSK. What about FT8? It doesn't cause any hiccups...
Since the mode does appear as FT4 in some places there doesn't seem to be much point in my editing anything because it looks like there's nothing to edit. It appears more likely that Cloudlog is extracting incorrect Mode data to create the files you upload to LoTW.