Yes, I've seen something quite similar. I have an ejb jar contained in a sar. In this case, it is not recognized as an ejb jar and is deployed by the JarDeployer. If I deploy the ejb jar as a separate deployment unit (not in the sar) then it works fine. The key point I see in my log is this:
2003-06-12 15:05:53,821 DEBUG [org.jboss.deployment.MainDeployer] Starting deployment (init step) of package at: file:/C:/java/jboss-3.2.1_tomcat-4.1.24/server/b2bintegration/tmp/deploy/server/b2bintegration/deploy/HFVSOrderComments.sar/2.HFVSOrderComments.sar-contents/HFVSOrderCommentBean.jar
2003-06-12 15:05:53,836 DEBUG [org.jboss.deployment.JARDeployer] No META-INF or WEB-INF resource found, assuming it if for us
2003-06-12 15:05:53,836 DEBUG [org.jboss.deployment.MainDeployer] using deployer org.jboss.deployment.JARDeployer@8bdcd2
I have verified that my ejb jar has a META-INF directory (in all caps) containing ejb-jar.xml and jboss.xml and it deploys fine standalone, so I'm quite certain this is a JBoss 3.2.1 bug (also seen in 3.2.2RC1). I've also tried wrapping the ejb jar file in an ear in the sar with the same results.
Luckily that grammatical error in the error message made it easy to find the location in the source: org.jboss.deployment.JarDeployer near line 103. If you haven't downloaded the source, here's one place you can see it: http://www.thecortex.net/clover/eg/jboss/report/org/jboss/deployment/JARDeployer.html
My take is that the DeploymentInfo's classloader is setup wrong, but that's as far as I've had time to trace into the code. I hope someone with more familiarity with the code can look into it.