I have the same issue.
I am new to ubuntu.
Running Ubuntu 9.10, GNS3 0.7, latest dynamips.
Qt 4.5.3, PyQt 4.6.1
Open project, hook on save to nvram and config.
open a .net file
make some config and doing a write.
When opening again
The only that is same is topology.
All configs are lost.
I had the same problem before when running 8.10 but this was solved doing a gksudo when opening the GNS3.
But this time it would not solve the problem. And I belive I should have all the write permissions when doing gksudo.
Never had any problems when running XP, Vista og Win7.
Will try to install again when the deb packing link is up again, but it is down for the moment:http://gpl.code.de/oswiki/GplcodedeApt
Others that have experienced the same issue?