I may have a curious problem. But as I use the geotools DataStore to connect geoserver to other services (i.e. WPS), I always get a problem, if geoserver and the other service (WPS) are running on the same tomcat instance. In case of geoserver 1.3.3 the DataStores are populated during geoserver/tomcat start-up. But as tomcat is trying to start geoserver and the dataStores are sending requests to initialize the registered DataStores, the other services on that tomcat instance are not responding. So geoserver is just staying idle while waiting that the DataStore is ready. I am aware of the fact, that this is somehow also a tomcat problem, because tomcat is not responding to anything while start-up, I guess.
Implementing lazy DataStore registration on geoserver side, could do it. But this issue is also a little bit related to geotools, as the DataStore is mainly geotools stuff.