Weird performance hit

I have two practically identical Debian-testing systems installed on
two harddrives on the same machine. I've compiled Postgres 8.0.3 with
exactly the same options on both. Both HDD use the same kernel, have
DMA enabled and so on. I have the same database and web applications
installed in both systems.

However, one application is for some weird reason taking a serious
performance hit on certain pages. There are some intensive joins and
selects there, but somehow one install manages a couple of seconds and
the other takes about 10.

Any ideas? I've tried copying Postgres and the repository over from
the good install, it does the same thing. Does this suggest that it's
not a Postgres issue?