If anyone happens to know an ideal iPod export setting in Cleaner 6.0, using a QT reference file out of FCP, you'd be much help. I ran into an issue with my audio and seem to have gotten lost tweeking my test exports and can't seem to find my way back.
Since Cleaner 6.0 doesn't support H.264, your only option is MPEG-4 Part 2, which isn't necessarily that bad for iPod if you are using the proper encoder, but Cleaner's MPEG-4 Part 2 encoder is not the one you would ideally use for this. Instead I'd recommend a number of the trialware apps under $50 out there for encoding video to iPod, Apple's own QT Pro iPod export settings, or best yet, Telestream's Episode software, which has the best MPEG-4 encoder bar none on all platforms.
When I selected iPod in the Output setting, I found an H.264 option in the Codec pull-down menu in Cleaner 6.0. It seems to work, however the default audio codec (QDesignMusic 2) doesn't seem to work with any video codec i select. Also, my only issue with exporting iPod out of QT Pro is the inability to change settings, i.e. frame size.
Do you have QT 7 installed on that system? There are a lot of known bugs in using QT 7 and Cleaner 6.0 on the same system. Supposedly, Cleaner 6.5 fixed a lot of those issues, but I haven't spent much time with Cleaner in the past year to really know if everything really is stable. Also, the iPod does not support the QDesign codec.
And if the direct iPod export option doesn't suit your needs from QT Pro, then just choose the MPEG-4 export option and match those settings as described in what the iPod can support on Apple's iPod Tech web pages. But again, I really do recommend other trialware options or Episode if you want to really want to control your video encoding for iPod.
You'd need Cleaner 6.5.1 to work with Quicktime 7.1.3. Much, if not most of Cleaner 6 and 6.5.0 is broken above Quicktime 7.0.4. 6.5.1 does have export to iPod presets (both H.264 and MPEG4) but I haven't tried them yet. The version of Compressor 2.x that comes with FCP 5.1.x also has iPod presets that you can customize. As Charles mentions, Episode is a good choice too (and has iPod presets).
After many test exports and setting tweeks in Cleaner 6.0 i was able to come up with a pretty nice file. I was able to stream and download in iTunes, however the crusher came when i tried to drag the video file onto my iPod and received an error message. So, i'm back to squar one which was exporting a QT reference out of FCP with a custom frame size (which takes considerably longer than exporting with current settings), then re-exporting the reference file out of QTpro with the iPod settings. It's a pain, but it works. If you have any other workflow suggestions that don't involve purchasing more software than i've already done.....holla back.