I have found that a complete uninstall using
synaptic package manager on applications don't
remove setup information. For instance on Thunderbird
setup and emails don't get removed. That is I think
because setup and data created for that application
are kept in your Home directory usually in a dotted
folder/directory. But if there is a problem with some
part of the application a new reload will restore the
compiled application and hopefully allow a restore for
use, as you found in Skype. I hope it continues to keep
working for you.