as Richard noted, a failing DWR is often the cause of what is experienced as a leaking jacket. I had the same thing happen with my paclite jacket at the sleeves. To find out if the jacket was really leaking or that the DWR had failed, I took it to a retailer who has a simple device to test the waterproofness of a jacket (using a a bit of water, a tissue to test leaks and a handpump to build up pressure). Not a drop of water came through at exactly the same spot where I had experienced possible leaks. For me it clearly showed what an effect DWR has on breathability and preventing condensation.
About the waterproof zips, I wonder how big the variation in quality is. My Arc'teryx paclite with the original waterresistant zips has never given me a problem, even in heavy rain. I agree they are a bit harder to operate although I neve experienced any real problems. The newer vislon waterresistant zips are supposed to be easier to operate although I haven't read a review about experience with it. BTW, as far as I know, Patagonia is still using these waterproof zips and presently, not a single jacket of them has an external rainflap.