The clouds persisted on staying last night so I took the oppertunity to sort out this low file size fiasco with the QC. Nuked the laptop and did fresh install of Win XP and only a few astro programs installed (cartes du ciel etc).
I then did some tests of 60sec dark avi's (cover left on camera), 15fps. The QC suite still only saved 7 odd meg files while K3CCDtools now seems to be working correctly

. Using the default compression codec 'Cinepak' resulted in 775 frames out of 899 being dropped = approx 4meg file. I changed the codec to 'Logitech Video' which resulted in 17 frames dropped from 899 = approx 97meg file. I then tried 'Full Frame (UnCompressed)' which gave 50 frames dropped (all were after ~30sec mark into the 60sec recording) out of 898, but weights in at 186meg.
Version of K3CCDTools is 1.0.6.460, I know its a very old version but it doesn't have the registration requirements the newer versions do

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Hopefully testing of real world targets produce similar results and not the lock ups/file problems that plagued me previously.