Pathfinder = overrated

Although it does have some really nice features, it has several strikes against it, which are the reasons I uninstalled it (although I do love some of it's features). Here are my quibbles with it:
1) when using Expose, the PF desktop slides out of the way, revealing an empty Finder desktop (or a populated one, depending on if you disable Finder's desktop or not)
2) PF's desktop does not remember icon location
3) if you move several items to the PF desktop, they end up being stacked on top of each other
4) adds many seconds to the system's boot time (or better stated, the time between logging in and the desktop being usable)
5) piggybacking on #4, adds a lot of time to shutdown/sleep

There are a few other minor issues that I can't remember the details to seeing that I uninstalled it shortly after trying v5...

I don't know what sub-version of 5 you were using, but many of these are addressed in the current 5.1.4:

1. Path Finder's Desktop now operates exactly the same as the Finder's Desktop. Specifically, it does NOT slide out of the way when using Exposé.
2. Though I normally keep my Desktop sorted by date last modified, I turned that off to test your issue. I moved several icons around, then quick and restarted Path Finder. All icons are in the place I left them.
3. Files moved to the Desktop no longer land on top of each other. They are placed appropriately on the Desktop.
4&5. I can't speak to this, as I very seldom reboot or log out/in.