Sorry for not submitting this bug in BerliOS, as I am having issues logging in there.
Anyway, the "Don't Set Up Automatically" flag in the Libraries tab of Project->Properties dialog does not save properly.
Steps to reproduce:
1. Create a new project
2. Click this flag and save the project
3. Close C::B and open the project again
4. Un-check this flag and save the project
5. Repeat step 3
6. You will now observe that the flag is still checked, when it should be unchecked
A workabout to this is to manually edit the project file and remove the disable_auto="1" entry.
My build string: Apr 17 2009, 15:25:13 - wx2.8.9 (Linux, unicode)