1. My laptop's external monitor's randr setting is currently --above because --left-of breaks the Intel video driver (Xubuntu 8.1 it caused complaints but worked, 9.04 it's performance is on par with a P-100 sporting a Cirrus 1mb video card)
2. Every morning I have to open a terminal and ifconfig my network address because Network Manager refuses to save changes (which is a step up from 8.1, which wouldn't even save network settings)
3. I have my 2 Windows partitions mounted in /media and manually mount external drives there as there appears to be no rhyme or reason as to when (or if) they show up in "Places" or a save as/open dialog.
4. I don't know what the berry_charge kernel module does, but it doesn't charge a Blackberry so I had to dig out the AC adapter.
5. When working with vector graphics, I have Illustrator installed in an XP virtual machine. Believe it or not, this is faster and more usable than Inkscape.
6. If I want to commit, I need to exit and restart Eclipse if it's been open more than 10 minutes otherwise Subversive endlessly claims it's "Running..." while doing nothing
7. It's nice xfce4-mixer in 9.04 lets me use my scroll wheel on it's icon to raise/lower volume, although I preferred 8.1 letting me use the volume keys on my keyboard

Sure it's a pain and there are many more I'm forgetting, but at least it's not Windows :)