This sounds silly, but did you publish the changes you made? I would Publish and then refresh my account:
"Refresh account" is sort of a "Have you tried turning it off and back on again?" type solution for Qualtrics. Any time I think, "Gosh- this should work. Why doesn't it?" Nine times out of ten, a refresh account works.

Alas, I did try that, but always a good reminder! Changes I make do show up (e.g. if I change the recode values to 1.3, 2.3, and 3.3, I see those reflected in the data export, but in the same pattern as above, the variable name as 1.3 appended etc and the recode values are still 1 and blank). Thanks though!

Sounds to me like an error with the system then- agree by all accounts you should be getting what you need. If you haven't already, make sure you contact support so they can escalate to engineering if needed.

Thanks, I'm trying to contact them now!

This is happening to me too! I recoded values and published the changes, but the later responses that came in did not have the correct recoding.
Did you ever resolve this issue?

I've been running into this same issue as well and have been working with Qualtrics Support for the past couple of days. In my situation I have recoded race categories into all separate values that I want to appear in the survey and just like what happens with you, if I select splitting multi-values instead of the recoded values appearing in the columns the values are all 1's or blanks. If I unselect splitting multi-values then the recoded values appear but in 1 column only. I worked with Qualtrics Support and unfortunately they said they currently don't have a workaround for what I want to do.
Probably will have to do a Matrix to get away with this. but if any Qualtrics Developers see this comment, you guys should really look into making "Select all that apply" questions being able to recode to what we want to do.