Thanks for the feeback (sorry for my late response).
I also noticed that xournal behaves differently in R1.7.1 and in R2.0. I am not sure what the problem is, file access seems to be slower too.
Since the xournal code did not change that much between the last R1.7.1 release and the releases for R2.0 I do not understand the difference in performance.
The xournal versions for R2.0 should be able to handle more files then the version for R1.7.1. But still the best thing is to use only pdf version 1.4 (compatible to Acrobat 5.0)
The Recent Files patch for R2.0 is still next in my planning (after a small improvement to the FBReader-port).