So when you used the auto-siphon with the cap on, were you letting the hops run free in the boil or did you have them in a bag?
I have to whole hop my lambic. But one of the reasons I'm considering switching to whole hops all the time is the knot in my hop bag untied in the boil for my ginger beer. The pellets excaped, turned to mush, and clogged my auto-siphon when I tried to transfer to the primary. I scooped as much of the hop mush out as I could before dumping it into the primary. But I know a bunch made it in there