every time Lawena loads its own config it backs up your own config in a zip file in your tf folder. My backup zip files never delete properly, but I haven't had any issues with them still being there and I just delete them when 10 or so pile up. Take a look in your tf folder and remove the zip files if they're still there
Also I'd recommend backing up your own config somewhere else as well before you start TF2. Friend of mine lost his entire config because of Lawena having trouble replacing the configs with the original ones again
Never encountered the 120 seconds issue, but maybe this'll fix that as well.
If not: Maybe it just takes too long to back up your config because it's too big of a file? It usually says so when your cfg files are too big to back up but maybe you don't get the error message for some reason. Try placing your cfg files in Custom elsewhere before starting Lawena. Maybe that helps