I have chosen to Combine Only while testing (because doing a full minify seems to make none of them work properly). IE was complaining about a script error, so I looked into it.
The following URL shows my footer file as combined by W3TC:
There are three relatively simple files being minified here (in this order):
On line 7 there is a ";28b" which does not appear in the source of any of those three files. Additionally, on line 37 there is a lone "0" which is not from any of those 3 scripts.
If it's doing a Combine Only, where would this extra data be coming from?