Note that the aptdaemon backend suffers from this problem as well due to [1] (patch).
A similar patch could be applied to InstallBackendSynaptic.py to track which packages were previously auto-installed and make sure they are marked as such afterwards. Otherwise, perhaps consider to just drop the synaptic backend and apply the python-aptdaemon fix.
Note that the aptdaemon backend suffers from this problem as well due to [1] (patch).
A similar patch could be applied to InstallBackendS ynaptic. py to track which packages were previously auto-installed and make sure they are marked as such afterwards. Otherwise, perhaps consider to just drop the synaptic backend and apply the python-aptdaemon fix.
[1] http:// bugs.debian. org/685044