My suggestion is actually to skip Synaptic. It seems to pull in some libraries and GNOME dependencies that, in my experience, bogged things down to the point of making the Pi unusable. Several times I couldn't kill X or even halt the system, I had to pull the plug and power it back up. Besides, even if it didn't lock the system up, using Synaptic on the Pi is no fun at all because of the strain it puts on the modest hardware. What's the point of Synaptic if you're not going to browse around, which requires a snappy user experience? Easier to just know what you want and use apt-get from the terminal.
Finally I just removed Synaptic and its dependencies (sudo apt-get remove synaptic followed by sudo apt-get autoremove)from the CLI before login, and now things are back to normal.