Can't see jobs dependencies on the large number of jobs.
This is supposed to be fixed in the release 11.3.5 INCR7. See problem AEIXP Pr#54 explaining that "With some versions of the JVM and iXp containing a large number of jobs, a users job flow view might not display all jobs and dependencies correctly".
WORLOAD AUTOMATION IXP version 11.3.5 INCR7
Update the JNPL file inside.
Change to <j2se version="1.5+" initial-heap-size="80m" max-heap-size="256m"