Oh wait, nevermind. I got confused between the free and premium versions.
I had the same issue. I updated to the new version yesterday and it completely stopped working. The plugin and font files were overwritten on my FTP site. I ended up having to revert back to the last backed up version (1.2.2) and got it working again. Majorly annoying! I’m posting on Pippin’s support forum as well… I recommend you do the same.
http://support.pippinsplugins.com/forums/forum/font-uploader/