You might already have found this, but in the 7334/44 hardware manual it is stated that "when (limit switches are) enabled, an active transition ... causes a full torque halt stop of the associated motor". The reason is that limit switches should never be reached during normal operation and rather are some kind of automatic emergency stop than a position feedback.
I think the only thing you can do is define software limits which should be located somewhat before the limit switches become active, and decelarate your drive as soon as it approaches these limits.
