I don't quite understand the claimed slowness of the iVI (Pro) remux. It takes less than 3 minutes for a one hour 720p video with Dolby audio (but no subtitles). Subler does not take under a minute to do the same thing unless it doesn't convert the Dolby audio. iFlicks takes around 2 minutes or less and is faster but it does much less. Subler is ok but it doesn't automate the process, have watched folders, etc ... In any case the remuxing capabilities of all three are really good. I can't imagine iVI taking an hour to remux anything. Something is odd.
Philip
Today, I've made some serious tests. (Late 2009 MBP 17" with 2.8 GHz c2d; source HDD is a 1TB one in the DVD bay; target drive is a Vertex 4 256 GB with 55 GB free) The source was a 16 GB MKV I've directly ripped from the Finland-only version of Iron Sky. It has four audio tracks (5.1 + 2-ch AC3 for the main audio + 2-ch AC3 Finnish + English commentary tracks) and a chapter track.
iVI Pro took 51m:24s to remux the video with all four audio tracks enabled in the output (most of the time was spent on audio reencoding and particularly adding). The other converters did fare far better:
Subler: 7m:0s (measured twice) (With fewer audio tracks, it's a bit faster: 5m:58s (to 2-ch AAC); 6:07 (to multichannel AAC) for one track and 6m:10s for two)
MKV2M4V: I couldn't test this with four audio tracks as it's only able to process up to two input tracks. The results with the latter are as follows: 12m:55s (measured twice) for two tracks and 13m:48s for one.
MP4Tools beta: 18m:50s. (With fewer audio tracks, it's considerably faster: 7m:40s for one track and 12m:50s for two)
AnyVideo Converter HD: could only test the one-track output as it doesn't support multi-track export: 4m:20s (2ch AC3 -> 2-channel AAC; iPad 3 preset, everything auto); 5m:18s (5.1 -> 2ch AAC, iPad 3 preset, manually selected 5.1 AC3 input); 8m:32s (to AAC 5.1 – the 1080p Mac MOV preset)
That is, iVI is particularly slow at converting videos with more than one audio track (if you want to keep them in the output). In this case, it was almost ten(!) times slower than Subler.
EDIT: when converting one audio track only, iVI needs 24m:18s to make the output file ready. That is, almost two times more than the second-slowest converter, MKV2M4V; more than three and four times slower than MP4Tools and Subler, respectively. Finally, it turned out to be about six times slower than AnyVideo Converter HD. (All with one track only.)