I think the CAPS 5.1 is already using Sun App Server and JMS Server, I haven't finished downloading it, so I can't be sure, only from the presentation.
I think it is better anyway, even though the builtin AS and JMS Server from Seebeyond is J2EE compliant, still I prefer to user the RI from Sun.
I think the out-of -box configuration of a CAPS installation uses the Sun SeeBeyond Integration Server, which is based on te SJSAS 8.x. However, the JMS server is still SeeBeyond IQ Manager, not the SJSMQ bundled in a typical SJSAS 8.x download. The SeeBeyond IQ manager does have a couple interesting features such as message journaling, and time dependency groups. The SJSMQ does not seem to have those.
Xuekun