I've had two cases recently where an old configuration file has been causing problems, and there's no clean upgrade strategy.

My wireless card was made by Broadcom, and I use the newer b43 driver in Linux. However, the new mac80211 drivers introduce a second network interface (used internally by mac80211) but with the same MAC address as the normal interface. And because it gets created first, udev puts this master interface into the place where the real interface is meant to be, and the real one gets called 'wlan0_rename'.

The fix was to look at /etc/udev/rules.d/z25_persistent-net.rules on Debian, and either add 'ATTRS{type}="1"' to the appropriate line, or delete the file, and let it get created on the next boot.

Another time this has happened was with X.org. Jonny Lamb pointed out that removing the 'VertSync' line from xorg.conf fixed (or at least hid) my recent ati driver troubles. On running dpkg-reconfigure xserver-xorg, the new XRandR support lets Debian create a much smaller config file than it used to, which is cool. However, people upgrading don't get to take advantage of it.