cable modem router and lan question

we are in the process of switching our internet access to cable. I have connected the cable modem to a linksys router. we also have a cisco 4000 series router that connects to our companies wan via frame relay. the problem is that certan network applications seem to be slow and drop the connection. I have configured the clients with 2 gateways one for each routers is thier something else ihave to do to make this configuration work properly