Here are some more information. Indeed, I should have provided them.
First : I still don't know what has damaged my original HD.
A "Clean Install" is the fix (not the answer to the origin of the problem). I needed a new hard drive because I need to keep it as a reference for the configuration of all the applications I use daily. Even though I use Time Machine to back up my data, I can't back up the setup of my apps. You can' simply copy over all your Application Support and Preferences folders. This simple can't work because some of the setups are tied to one instance of MacOSX. When you install the OS, unique informations such as UUIDs get created and you can fix old prefs to work with a new OS install. I have some 500 Unix apps and modules I need to recompile. I can't just copy them. For instance, some are tied to the dynamic temporary directory in /var/folders.
Anyways, I needed to keep my original hard drive for reference. Most of the "standard" users of a Mac will be happy with a Clean Install.
The problem I experienced is crazy: The UI freezes a fraction of a second every 3 to 10 seconds then restart catching up what was delayed during the freeze. On movie playback, it's like when you see a TV ad where actions accelerates to skip non important moment and then slows back down. Here, the frames past the freeze are played back quickly until it catches the lap. All apps were impacted, even the genie effect when the Login Window appear after a reboot. No process hogging CPU, nothing to be monitored ... just "stand still", "catch back", "stand still", "catch back". It's not fun when you move a window on the Desktop : it drops. No fun when you right click : Contextual menu closes .... Just like when somebody is poking you in the back when you try working !
That problem did a few time not happen on the machine when stored shut down and being cold. I comes up after being warmed-up and RAM loaded. I swore to the repair guys that it could be only a hardware problem. Proof it wasn't :-(
I also prefered to get a new drive, in case the HD had indeed a nasty hidden interface failure - even though all evidences showed that the original hard drive had no failures (hardware bench tested) and a Clean install (plus new HD) removed the issue.
I will only get the real end of the story after I clean install the original HD. Problem is that I don't have an DVD with 10.6.8. It's a downgraded Lion machine. AND I can't use Lion because there is no Spaces (I use 16 spaces (2 * 4 on dual displays). But that's another story.
I had to take two days of vacation the time the machine was under repair and it took me three days to install back all my stuff. I lost 5 days of work.