But without any netapp-side DNS debugging tools (AFAIK) it's hard to know exactly what the problem is.
For what sort of tools are you looking? An RFE (15458) has been filed, but it contains only your mail message, no further details.
I've improved the error messages for the NetCache 3.3.1 and the ONTAP 5.3 release, to give more details (and to shut up about DNS servers not in the appliance's domain - for a NetCache box, reporting *all* failed DNS lookups really fills the log file up with gunk, given that the chances that at least one DNS server out there on the Big Wide Internet is down are pretty good; if you want the option to report about "foreign" DNS server, let us know, so we can add that as an option).