I have this issue with Audacity as far as I can think back. I even remember 
having similar problems back on Windows 98. I'm currently using 1.3.9 Unicode 
on Kubuntu. The problem was always there throughout the years. sometimes it 
would let me work on 2 or 3 consecutive soundfiles and then it would just not 
work.
Starting from the commandline did not help.
I've tried to install ESD and use this -but this caused complete havoc on my 
installation, so I revertet back to ALSA/Portaudio.

Steps to reproduce:
1. load a soundfile. I usually load wav files of about 25-45 min length
2. either:
    - cut a few seconds or minutes off the end
    - select a section and perform an effect on it
3. export the whole file. It does not matter wether you save as mp3 or wav

I usually see 100% cpu after step 2, then I know it will die in the next step. 
The export function lets me see both dialogs, the one to set the tags and the 
one to select the file location. but after this ...
Sometimes it had helped if I start up audacity and close it without actually 
changing a file. But since recently nothing seems to help. Advice?

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Audacity uses 100% CPU on opening any file dialog
https://bugs.launchpad.net/bugs/250367
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