Vista - Dropped frames at end of Nero Digital files

I used to have Nero 7. I think it had Recode 2, which always worked, 100% of the time. There were some finicky things about it, but nothing that ever affected the files it produced. Well, it used to go over the quota on a regular basis, but whatever. The ability to encode DVD directly to MP4s for an iPod is supremely brilliant.

I recently upgraded to Nero 9(.2.6.0) with Recode 4(.2.16.0) and have installed the most recent update pack. Since upgrading to Recode 4, I have had a persistent problem with the resultant files having the last about .5 seconds of video missing while audio is correct. In QuickTime and iTunes, the lost frames show as white frames, in ShowTime and VLC Player as black frames, and on my iPod as the last good frame. These lost frames completely ruins the fidelity of the music and other video I'm encoding. This issue also occurs when using the Nero Digital profile at any bitrate.

In addition to the above issue, Recode 4 does not properly auto-identify interlaced video, so this setting must be manually set for every title. Resizing refuses valid input and resets my input to a smaller (and sometime off-aspect ratio) setting, for example: I'll input 640x352 and it rejects it for 624x416, which is off-aspect and a ridiculous size for my iPod, as 640 is the 320 pixel width times two. however, 320x176 is permitted.

These problems effectively render what was an amazing piece of software in older versions into a completely broken tool. I have Vista Business x64 SP1 on an AMD Turion64 and 2GB Ram. I have completely uninstalled the product, downloaded and ran the Nero 7 and 9 cleaning tools, and reinstalled. My first test file after that worked perfectly. I did a batch of six titles, five of which had dropped frames; subsequent testing has yielded the same. I must reiterate that with Nero 7 and Recode 2(?) none of the problems with Recode 4 ever occurred, so I'm confident Nero will present a solution and quickly.