I seem to be having the same issue (FV3.3). Whenever my search or query results in 1,000 or more records I get the "Error #1009" error. I've changed the "maximum number of records returned by the server" for the service that I'm running the query/search against from 1,000 to 3,000 in ArcCatalog (the most records returned for the service is 2,910 records). Is there any other settings I need to change? I didn't see a max records setting in the geometry service.
Thanks,
Joe