This is happening to me as well, using Arc 9.3.1. Hollie is actually using our tools, so this problem might end up effecting a lot of our users, so any insights would be appreciated.
Here's a bit more info. It's happening within a Python script (actually, a couple of them) where I've done a bunch of raster calculations (very different in each script) and in the end aggregate the results using Zonal Statistics, where the zone file is a shapefile of watersheds. One odd thing I'm seeing in one of the rasters that fails with this error is that when I look at its Statistics, the Mean value is 1.#QNAN, and Calculate Statistics will not work on it (CS tells me that it's invalid when I try to add it to the dialog box.) If I turn the watershed file into a raster, initial tests are showing that Zonal Stats can work, but Zonal Stats as Table does not (using either shapefile or raster zones), but returns a different error:
ERROR 010067: Error in executing grid expression. Zonal statistics program failed
Failed to execute (ZonalStatisticsAsTable).
Now, the QNANs first appear when I do a Lookup_sa on a raster with a bunch of fields, created by doing a join between a watershed raster and a table, then a CopyRaster to a new grid. This new grid looks fine and has proper Statistics. The resulting Lookup values and maps look good, but the Statistics say Min 89, Max 1701, Mean 1.#QNAN, Std dev 0, Classes 0.
Zonal Stats as Table seems to work fine on rasters that have proper statistics, but not on those with a Mean of QNAN. Could be coincidence, but it's the only thing that looks obviously amiss.
~ Stacie