Excerpt from a post on JDEList.com by Colin Dawes:

You CAN NOT use the jt400 from the client access folder.

You need to use the jt400 that is on your iSeries. The 2 versions are not the same and you’ll get some hanging if you use the iSeries Access version.

The jt400 on the iSeries is located at:
/QIBM/PRODDTA/HTTP/PUBLIC/JT400/LIB/JT400.JAR

Usually you need to copy this to the following location on Windows:
WebSphereAppServerlib

I say usually because sometimes during the installation prople point the installed to the iSeries Access Path. In this case the WAS variable will be incorrect and you either need to (1) Change the variable in WAS or copy the jt400.jar from the iSeries on top of the jt400.jar that came with iSeries Access.