Bill,
When you say that the Cisco is providing clocking, is this on a completely internal circuit (i.e. just a cable or a conditioned line between the Cisco and your card)?
The reason I ask is because if it's a T1 provided by a telco, then you should be using external (network) clocking on both ends of the circuit because your devices do not speak directly to each other--they each speak to telco equipment. I do not have any experience worth mentioning with data T1's since they've always either worked or not worked. But I have seen oddball things like this with T1 voice trunks (working half-assed).
Please forgive me in advance if I'm out of my depth here.