Comment 11 for bug 1328586

It may very well be this bug is not about possible issues with apt (apt-ftcarchive).

I point out again that this bug is not present when using gnome-shell and mutter versions 3.10 or even lower.
It can be experienced only using gnome-shell 3.12 or newer.

Another thing to remember is that apt itself works just fine from terminal and at the same session when synaptic is frozen.
Commands like apt-get update and apt-get upgrade are working all the time.