Bug is 100% reproducible with these steps:

STEP: In #1 fresh workspace create simple java project with two simple archives in it
STEP: Open #2 fresh workspace, add JBoss AS 7 server in it
STEP: Import project from #1 workspace
STEP: Deploy first archive into the server
ASSERT: Archive is properly deployed
STEP: Deploy second archive into the server
FAIL: Archive is not deployed at all

Note that this bug is not dependent on which tool is used for manipulation with archives (Project Archives explorer/view)

I've just found out that there is another workflow how to achieve a different bug (but I believe the same reason):

STEP: In #1 fresh workspace create simple java project with two simple archives in it
STEP: Open #2 fresh workspace, add JBoss AS 7 server in it
STEP: Import project from #1 workspace
STEP: Deploy first archive into the server
ASSERT: Archive is properly deployed
STEP: Remove archive from server
STEP: Deploy second archive into the server
FAIL: First archive is deployed into server, not second as it should

open .packages file and change

<property name="org.jboss.ide.eclipse.as.core.packages.ModuleIDPropertyKey" value="1350308437788"/>

for first archive to

<property name="org.jboss.ide.eclipse.as.core.packages.ModuleIDPropertyKey" value="1350308437789"/>

save the file and restart eclipse right away. It is required or archives model will serialized over your changes at next deployment.
After restart the issue is cannot be replicated anymore.