https://jira.jboss.org/jira/browse/JBIDE-3641 addresses this issue.
So far things look pretty solid. I believe everything in the patch can 
be committed for a GA. The only issue here remaining, as is mentioned in 
the JIRA, is that the I can't seem to change the runtime component name 
without running into weird issues. When I try to make a 
runtime.eap.component instead of runtime.component, it all goes haywire.
The reason this is important is that eventually we may have a 
significant difference between EAP and AS, with the same version name. 
Therefore they need different runtime-component names.
However when i change the runtime-component name for the eap server to 
runtime.eap.component, the EAP servers don't appear in a new dynamic web 
project list (and, oddly enough, the two JDK's I have in my workspace do 
appear... as a runtime... ... ... ?!?!?!)
However, because a runtime maps to a runtime-compnent, I believe as long 
as the wst.server runtime id's are set, the runtime-component details 
can be changed later.
Patch is attached on the JIRA. Let me know if it's solid.