One thing that I noticed all the offending files had in common was that they were either videos or audio files (fly, mov, mp3) and not imagery. I exported the originals (I use a Managed Library) and converted them with QuickTime Player to MOV format and then imported and then replaced the file to which the problem then subsided.
I think it might have been down to the software I originally used to convert the videos, as I mentioned some were .mov and there aren't a lot of those things flying about on YouTube, I know I would have converted it (especially when the original file name has "YouTube" in it), of which QuickTime 7 would have been used because I could embed metadata, this obviously the course I took before Aperture accepted video formats because I notice that Aperture cannot import existing (custom entered) metadata into it.
What was really wired was that when importing files which were of the same name as the original (the one causing problems) that the file would disappear. I double checked by making a new copy of the file again and watching it import only to see it disappear before my eyes and nowhere to be found but in the Trash can, but why?
The difference being, that I can tell, is that unlike the FLV files the MOVs were always going to be MOVs (I always output moves as MOVs) and so Aperture must be doing something automatic when the conditions are right i.e. the file name matches and sends them strait to the Trash!
Even if I change the name of the video before importing the file it will keep doing this, not only that but the file cannot be traced back to it's location on my HDD, it just gets sucked in a lost inside Aperture, turning into a muffled (what seems to be unprocessed) image thumbnail of the video.
But it gets even weirder as I place those files into a folder for inspection (as the Trash can won't allow for metadata inspection, for some reason the pane is greyed out and inaccessible) those videos (still registered as such) turn out to be fuzzy pictures, not pliable at all.
However those conventions were with QuickTime X, using QT7 I was able to create (and then rename) a copy of the movie file (at almost exactly the same size in MB and so nothing was real changed!) and it imported okay. Now you might be thinking it was the way it was encoded, but one of those MOVs was always a MOV and came from QTX as a screen recording!
I don't know what's going on?! It seems to be that Aperture still has issues with other formats other than imagery, which was a major feature of the third release.
Now there are only two audio files that process and are done in the blink of an eye, I can live with that, thanks for your insight leonieDF.
