I have the exact same issue. 
One of the cores shoot up to 100% when making a test sound, a test call, and a 
real call.
Skype is configured to use pulse for soundout and ringing.

By setting soundout and ringing to use hardware (plughw:Intel,0 for me)
solves the CPU usage issue, but Skype will hog the sound device. i.e.,
no other application can access the sound device.

Ubuntu 9.04 AMD64
Skype 2.0.0.72-1  (from http://www.skype.com/go/getskype-linux-ubuntu-amd64)

I had no such issue in 8.10 64bit.

** Tags added: cpu jaunty pulse skype

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Skype high cpu usage on Ubuntu 9.04 64-bit
https://bugs.launchpad.net/bugs/362203
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