It's the thing with upgrades: Things are newer, often better, but sometimes not always compatible and working the way you were used to in the previous release. I stumbled over the same thing when I upgraded my Ubuntu 8.04 to 8.10. I installed the latest Skype-package too and chatting seemed to work like a charm...
Until I tried to actually voicechat. Skype showed problems with the sounddevices and even trying to set them manually wasn't really successful, especially when you had other applications (or even skype itself) access the sounddevice at the same time.
It turned out the problem is a new package included with Ubuntu 8.10 called Pulseaudio. I haven't heard of it so far - but to be honest I'm not keeping myself too up-to-date with all the latest additions and changes done in current Linux-systems. But it's not surprising that another new subsystem/daemon/framework emerged by now. Strangely, when setting the audio-device in Skype to "pulse", it actually did work - but used up all my CPU-power, leading to strange delays.
Looking at infos like here http://www.pulseaudio.org/wiki/PerfectSetup#Skype, I see there are alot of things to fiddle with, but I ended up simply doing this:
killall -KILL pulseaudio
/etc/init.d/pulseaudio stop
Though the init-skript didn't seem to be doing anything. I haven't investigated any further to be honest, but killing the pulse-daemon made the option "pulse" not appear in skype anymore. And just leaving Skype's settings at "default" after that ended up working perfectly. I haven't experienced any drawbacks of disabling pulseaudio so far, but I'll inform myself alittle more about the whole thing and update this thread then. For now I'm simply glad I have a solution to this strange behavior.
[update]
Ok, after checking some more I decided to get rid of Pulseaudio. I found a very nice, comprehensive guide for 8.10 here:
http://idyllictux.wordpress.com/2008/10/29/alsa-instead-of-pulseaudio-for-ubuntu-810-intrepid-a-non-destructive-way/
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