Changing the query string to exclude a certain category from the home page works for me, but it seems as though this makes the "posts per page" parameter more of a "maximum posts per page" parameter.
For example, if I'm excluding category X from my home page, I query for 5 posts per page, and 4 of my 5 most recent posts are in category X, then only one post (the only post that isn't in category X) displays on the home page. Likewise, the "older posts" pages display a maximum of 5 posts per page rather than simply 5 posts per page.
Is there any way to query for posts in such a way that my category X articles do not add to the posts per page count? I would like to see exactly 5 posts per page on my home page, obviously excepting pages where I have less than 5 posts not in category X.