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I use Cleaner XL every day for encoding. Even with the manual you have to account for a little bit of a learning curve. The interface is also slow as molasses too, but it does do a great job for batch processing to multiple formats, eg. mpeg and wmv and real and in multiple bitrates and sizes (320x240, 640x480 etc). It took me months figure out how and where to save the encoding presets, but now that that is done, it is pretty quick for me to set up encoding jobs. Cleaner XL will let you add watermarks as .pngs in the encoding process which is much better for the integrity of the watermark text than adding them in your editing program beforehand and then compressing them when you encode.
Tip: You have to manually edit the encoding presets with a text editor like notepad to make custom mpeg-1 video frame sizes other than the available presets in the interface. (Eg you want a 512x 384 or 192x 144.) Unbelievably the designers left out a way to set that in the encoding options like you can with wmvs!
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