At last my blip problem has come to an end, and I think I found what caused it... I don't pretend to know all the details about H264 compression, and I don't know if this solution will help others, but here are the details:
Sources: AVCHD files coming from a Sony Handycam, and from my own Sony DSC-HX5V (1080i/50, High@L4.0, 16MB/s , MTS container)
Symptoms: never had a blip until recently, as I was rendering in 720p/25 through external x264 vfw codec. When I decided to render in 1080i/50, I noticed, like others, a degradation wherever VSX3's built-in AVCHD codec was summoned (would that be the full file, or only transitions, effects, and title frames when Smart rendering was activated). But there were no blips to be seen in the final result, at least until I decided to view the files on my Samsung TV (Series 7 LCD), through USB and the TV built in player.
In short, at least in my case, I have the exact same blips described everywhere when I play the video in Samsung player. But playing this same file on a Windows 7 (Pro, 64 bits, fresh install by me, all built-in codecs untouched) under Windows Media Player (?!) gives a perfectly smooth, blip-free result.
Comparing the details between my original files and the VSX3 smart rendered file, I noticed (through MPC Home Cinema player's detailled file properties, although MPC can't play these files properly) a weird difference: my MTS files have a "Format settings, GOP: M=1, N=26" that has just disappeared on VSX3 end result, although Smart Rendering has copied raw segments in it. I may be completely wrong here, but this seems weird, as this would mean that the final smart-rendered file contains a mix of segments with a defined GOP of 1/26, others (VSX-generated) with some default (I guess) GOP values, and a possible explanation would be that some players accept some kind of a dynamic GOP (Win7?), while others don't (Samsung Series 7 and many others?), and would blip when a cut happens at the worst moment within a GOP.
Now, why does VSX3 also produce these exact same blips when Smart Rendering is deactivated, I don't know - but it sure does.
From there, all I thought was needed was a conversion tool that would accept my blip-full VSX3 generated files and ignore the blips in there, just like my Media Player does, re-save them in 1080i/50 without too much loss, and with no blips...
Solution that works like a charm for me:
Render my videos in VSX3 with smart rendering on, to preserve original quality as much as possible
Re-compress the resulting hybrid MPG h264 file with XMedia Recode - the best, easiest, and more configurable tool I've found to do 1080i/50 x264 compression (since x264 normally doesn't do interlacing).
I personally use XMedia Recode with the following settings - still have to do more tests:
MP4 AVC/H264 firstname.lastname@example.org, 16MB/s, 2-pass average bit rate, interlaced TFF (for a MBAFF result), deblocking on at 0/0, CABAC on
And while I'm at it, I often duplicate the audio channel to get one with MP3, the other in AAC or AC3 (MP3 stream helps if you want to hear something on some devices like Samsung TV without having to turn the volume to max)
Resulting file (after long rendering time, I must say) is slightly smaller than the VSX3 source, which makes sense, and visual result is really, really, close to the original. It plays perfectly, with no blips on all my devices - only VSX3 can hardly swallow it back on the timeline (due to MBAFF?): it works, but edition becomes damn slow.
Again, some of my conclusions on the root causes may be completely wrong, but at least, I now have what I need to produce good results that stay within video format standards. Almost good, that is, because the transition, titles, and effects sequences generated still suffer from VSX3 built-in h264 encoder, and it's still a real problem to me. So, I'm keeping my sources, in the hope that future versions will either improve quality by default, or include fine-tuning possibilities for h264 interlaced encoding....