Jython’s Exception class does not inherit from Java’s base exception class - so exceptions thrown in Java code (ie, everything written by Inductive Automation) are not caught by Exception clauses. You have to catch both possible exceptions:
import java.lang.Exception
try:
# something something something
except Exception, e:
# jython exception
except java.lang.Exception, e:
or
import java.lang.Exception
try:
# something something something
except (Exception, java.lang.Exception), e:
#pass