I had a similar problem with the NoClassDefFoundError in JBoss EAP 6.1 when using classes from sapjco3.jar in an EJB (annotated with @Singleton and @Startup). Besides that I also received an error saying that the native library was already loaded in another classloader when republishing to EAP or restarting the deployed module.
My solution to both problems was to include sapjco3.jar as a global JBoss module.
Step 1
I created the following structure inside EAPS's \modules folder:
com
--> sap
--> conn
--> jco
--> main
--> module.xml
--> sapjco3.jar
The contents of module.xml:
<?xml version="1.0" encoding="UTF-8"?>
<module xmlns="urn:jboss:module:1.0" name="com.sap.conn.jco">
<resources>
<resource-root path="sapjco3.jar"/>
</resources>
</module>
Step 2
Adding the module as a global module in standalone.xml:
<subsystem xmlns="urn:jboss:domain:ee:1.1">
...
<global-modules>
<module name="com.sap.conn.jco" />
</global-modules>
...
</subsystem>
Step 3
Create or edit file jboss-deployment-structure.xml inside EJB projects META-INF to contain the module. My file looks like this:
<?xml version="1.0" encoding="UTF-8"?>
<jboss-deployment-structure>
<deployment>
<dependencies>
<module name="com.sap.conn.jco" export="TRUE" />
</dependencies>
</deployment>
</jboss-deployment-structure>
Step 4
Configure Maven dependency as scope provided, so that we can work with sapjco3.jar inside the workspace but not have it inside the deployment.
<dependency>
<groupId>com.sap.conn.jco</groupId>
<artifactId>sapjco3</artifactId>
<version>3.0.10</version>
<scope>provided</scope>
</dependency>
That is what I recall so far to make it work, maybe this is helpful for you or anybody else.