If you close Synaptic by clicking the X in the upper right corner (which may be something my window/desktop manager (LXDE) attached), it's not the same as doing File->Quit. The lockfile doesn't get removed, so apt commands don't work. I had to pkill synaptic, then bring it back up and close it from the file menu, that removed the lock file. This should happen on window close I think, no matter how the window gets closed.
Alan -- ------------- Education is contagious.