There must be a change, a program don´t stop working without a reason. The firewall can´t be the reason - you don´t use the same one for Linux and Windows... did you upgrade to a newer Limewire version, perhaps a beta? Do you have other problems with your internet? The router could be the problem but there must be a reason for this... did you change the settings?

Are Linux and Windows reacting the same way or is there a difference?

Morgwen