When you execute a CLI command the prompt will not return until the command is complete. If the command takes several minutes you will be staring at a blank console for several minutes if the command doesn't produce output. How long did you wait before concluding the prompt wasn't coming back? Sometimes the prompt doesn't show afterwards, in which case a simple press of <Enter> will bring it up.
Secondly, have you searched and destroyed lock files? When programs such as rpm and, I believe, apt start, they first look for their lock file. If it exists they immediately exit (with or without a warning depending on the programmer's thoughts). If it does not exist they create it, and then when they are finished they delete it. The lock file will either be an empty file or it might contain the PID of the process, but its main function is to exist if the program is running. This is important because only one package management program should run at a time, since otherwise you could try to install a program and remove its dependencies at the same time and defeat the integrity checks built in to ensure you don't break your system. Also, the rpm database could be corrupted if two applications can open and edit its files at the same time. So lock files are used to ensure you can't run the same program twice simultaneously. If the program crashes in the middle, or the power fails, the deletion of the lock file never happens, and next time you try to start apt it will refuse to run. For Synaptic, this means it will not be able to read the package lists when it starts up, as it uses apt-get to do that and apt-get won't run, so it waits for a non-running program to report its results.
You therefore need to find and remove the lock files.
Genomega has told you where the rpm ones will be, if they are there, but it is probably the apt one you need to find. I know there is one at /var/cache/apt/archives/lock and another at /var/lib/apt/lists/lock, but not sure whether they're the ones, which is why I suggested renaming rather than deleting them.
