Yea this plugin has some bugs which several of us patched in our own forks and chatted about it several months back. One day all of us will bring our working forked versions together for a final new version but for now it works solidly for all my sites with the latest WP release.
It's been a very long timer now so my knowledge of this plugin under the hood is very hazy so i cant recall much but to fix the expire time issue you could go into your database file and modify the time directly there. We tested that back then too and that worked fine -- for those who were a bit apprehensive of touching php.
Out of curiosity are you having wp-minify pull the jquery file from a remote location or is it local on your server? Make sure it is being included. Also I do recall jquery using a line such as "+ ++n" which wp-minify minified to "+++n" which is a syntax error. But it might be something else.