I had originally set my site up with the default for hyphenated tags, and it was set like this for the first few weeks.
I then enabled the Use comma as the only tag separator option and the Q2A tag suggestion no longer works. It will only match one-word tags up to the space or hyphen.
This behavior does not occur on a Q2A site set up from the beginning to use comma as tag separator.
EDIT: I am editing this question because the issue ended up being different from what it appeared. The issue is that Q2A is returning just the 200 most popular tags, so if the user is entering a tag that is not in that list of 200 it will not find a match. My explanation is below.