Dave, what else were you wearing on your legs ? Gaiters / overtrousers ? I know you appear to think that your boots are faulty, but in all honesty, I think that 2 hours' waterproof in bad conditions isn't bad. Also, I'm not trying to belittle you or your choice in boots in any way, but your "expensive" Meindl's aren't really - as Meindl boots go they are pretty much bottom to mid range boots and more akin to high-top approach shoes than boots .
Chris - nobody is really talking about holed membranes here are they ? The fact is that when a jacket or boot lining wets out it will leak and/or vapour will fail to pass through it resulting in wetness inside. The DWR can be replenished on a jacket but NOT (in my opinion) in a boot liner - simply because the liquid CANNOT reach the lining . any waterproof treatment applied to a fabric boot simply gives the outer a certain water-repellency.
My original gripe is with people who say that a goretex boot WILL let in water, but an identical boot without a goretex lining will stay super dooper dry if you nikwax it properly. IT WILL, but then so will the one with the goretex lining..