Most Web users, especially those drinking from firehoses like HN, don't actually read pages end to end, they skim them looking for interesting bits worth reading. This is why they're skipping page 1 without reading it, and since your navigation system doesn't allow "skimming", you're seeing people giving up in frustration.
Another way of looking at it: I still have no idea what pen.fm is trying to do, and the only thing I'll remember about it is the broken navigation system. This is probably not the first impression you want to give people.
Even more fun, the bigger scheme includes the ability to export these stories directly on-demand to different e-reading formats (epub, mobi, pdf). So, if you want PDF, you'll get it. With enough content in the network, we'll take on content discovery in a big way so we make sure you don't waste your time having to skim so much.
This UI is the lite version of that magazine.