I am using Rhythmbox to sync my iPhone (3GS 16GB) which is running IOS 4.0.2.
Music/podcast sync works fine, but the order poscasts appear in (on the device) once synced seems to be random. This makes it very difficult to find the next episode if you have a large number from one feed. The order in Rhythmbox us correct (chronological).
I am running Ubuntu 10.04 with libmobiledevice1 from https://launchpad.net/~pmcenery/+archive/ppa
libgpod is also at the latest version from the pmcenery repository (original comment mentions libmobiledevice, but this is because I originally raised the bug against them, and copied and pasted it here).