when you tap on one it won't take you to that page
Yes it seems iOS5 web browser is different & does not scroll any more.
In iOS4.x it loads up PDF's as if they are a web page, so you could internally scroll them quite easily. Now it seems to load up PDF's as some kind of document that you can't use javascript on.
We've fixed this problem in the current beta that we are testing. Hopefully we can release it very shortly.