I'm sorry, but I've never tried using a 2nd-level cache like that for multiple JPA persistence contexts. I'd be very surprised if you could do that, because each persistence context would likely be stepping on the other in the cache.
Please don't be sorry. As I said this is not a modeshape problem. I will do my own homework and do some more investigation.
One quick solution was to define another cache in infinispan-configs.xml and use it for the modeshape configuration.