Just want to bump this one up. Probably shouldn't have posted just before the Christmas holiday.
I'm on Mac, and don't know whether this will help a Windows user, but rebooting the computer resolves most of my problems (and I have plenty) with AME. You could also try deleting the prefs.
I've noticed that some codecs cause more problems than others. AME isn't the app I'd use for general purpose transcoding. It's too unreliable. Quicktime Pro or MPEG Streamclip is what I'd go to first. They don't just stop in the middle, exit unexpectdedly, or produce erratic results.
I've seen an AME export hold a frame as you described when there were blank spots in the timeline. Zoom in on the problem area to frame level and see if there is perhaps a gap in the timeline at the point where it freezes.
To reset Premiere prefs, hold down the SHIFT key while launching Premiere.
Hope this helps
Safe Harbor Computers
Thank you all for your responses. For the benefit of anyone in the future who has this same problem, here is the solution (provided to me by Adobe tech support).
In Windows 7, click on start
Type %appdata% in the "search programs and files" field and press "enter"
Open Adobe folder
Open Adobe Media Encoder folder
Rename the" 5.5" folder "Old 5.5" (or delete it)
Now everything should work fine.