Well I've finally fixed my problem! This has been a thorn in my side since day 1.
The problem appears to be caused by the adapter I'm using with my Foxtel box to convert the SCART plug to S-Video. When I used the STB's "VCR in/out" port with the provided cable (unfortunately this forces me back to using Composite), I no longer get the problems with high white scenes causing flicker and audio drop outs!!
I found this thread, which pointed out that Maplin converters have problems with signal levels, and when used with a Hauppauge capture card, can cause lots of problems. I don't actually know what brand the SCART adapter I'm using is, but when I stop using mine, I no longer have this problem. I'll have to look at another method of getting S-Video out of my Foxtel STB..
http://www.hauppauge.co.uk/board/showthread.php?t=10549
And some examples linked in that thread (although not quite what I'm seeing):
http://www.hauppauge.co.uk/board/showthread.php?t=7249
Hopefully this helps other people, although I'm not sure it exactly relates to the OP's problem..?