I've seen the same problem when I added multiple jar's to the classpath suffix.
I looked at it in the debugger: even though the jars are separated by newlines in the Admin Console, in domain.xml the newlines are replaced by a string like ${path.separator}.
This path is passed to the classloader used during deployment as is, i.e. the path is not broken up into separate urls to the jar files. The File class could not make a canonical path from this file url containing "${path.separator}".
When I checked the file it was looking for was actually not important, it was just checking whether there was a META-INF/services/javax.xxx.YyyFactory resource in the classpath, probably used by JAX-RPC. I suppose it is safe to ignore as long as you don't rely on such file, as long as your application does not rely on the jars in the classpath during deployment.
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