Misnamed apps? Wrong versions? Fix here
Taking some advice I saw on the BAW forum one step further, I deleted the entire /data/boot-cache directory (after doing a nandroid backup of course).
Took about 3-4 extra minutes to boot up, presumably to recreate the contents of the directory, but now all of my apps are showing the correct version, correct icon, and correct name. Haven't run into any issues yet.