Yes, I have received your email; now I also have a better idea what the problem is.
There’s an important difference between ACA and the latest APT version – when using the “category” taxonomy, term names should no longer contain category IDs. Categories are now automatically created if the term name doesn’t exist in the particular taxonomy.
So basically you need to replace these IDs in your keyword sets with category names – then categorizing posts should work as expected.
Since you have quite a lot of keyword sets, doing this manually would take forever, so I suggest the following:
1) Find a way to export your category names and their IDs.
2) Export your keyword sets.
3) Import both to some spreadsheet editor, sort these items so that category IDs correspond with term names, replace the term name column in your keyword sets with the other column containing category IDs.
3) Save the file as CSV and import it back to APT.