ZHLT 3.0 has a small bug in the hlrad tool. Adam mentioned that it would be fixed in the next few days...
As long as you don't 'Opaque' any of your func_entities, it works well.
The quick fix is to use ZHLT 3.0 hlcsg, hlbsp and hlvis and use an older version of hlrad, possibly XPCagey's rad or even the old 253 v1.7