Version:           Gideon 3.0.0a4 (using KDE KDE 3.1.1)
Installed from:    Gentoo Packages
Compiler:          gcc 3.2.2 
OS:          Linux

From main menu with a C++ project, do the following:

Project --> Project Options --> Configure Options --> C++
Add some custom options such as -I/usr/qt/3/include
Click on the [...] on the Compiler Flags line.
Modify some settings (e.g. add a warning)

Expected result:
Custom option such as -I/usr/qt/3/include would stay in the textbox.  The additional settings added by selecting them in the [...] options would be ADDED TO the list (or removed, as appropriate).

Alternate expected result:
Gideon would warn me that it was about to overwrite the settings I had configured.  This would be a nasty workaround but better than the current behaviour.

Actual result:
Custom options I have previously entered are removed entirely.