Its because the game when hosting its own server introduced a huge amount of extra settings which get saved back into your config (which then runs out of cvar memory). This cannot be avoided, you have (temporarily) converted your workstation into a server.
A clean solution would be to delete the jampconfig.cfg and start again. Run the game, connect to a server, put all your settings in and once you are happy with all your controls, binds, sound, graphic and network configuration save them to another cfg with the /write <filename> command. That way if/when you lose the lot you can restore your preferred settings with /exec <filename>. Use your own name, or perhaps "backup", so you'd do /write sam, and /exec sam.