Search in webapp converted from classic to claims

Hi,

I converted my webapp from classic to claims. When using classic my search index had >600k items. Now it has <60k. The only specific search advice I found was to ensure that the policy for the web app must be updated by re-adding the search crawl account in claims format, which I have done.

Now, clearly the crawler is working as I have items in the index, however we are getting complaints of incomplete or missing results which is evidenced by the relative size of index.

I have some rows in the ULS:

01/17/2011 10:45:33.25 w3wp.exe (0x2350)                       0x2330SharePoint Foundation         Claims Authentication         g220UnexpectedNo windows identity for uopnet\XXXXXXX.e7f6c99a-5699-4529-a60c-a56ee32c60ea

My content source is set to a custom zone with WIA/NTLM enabled. I also turned off client integration in that zone based on advice seen elsewhere.

I am planning to build a new search service application as I am otherwise out of ideas.

Thanks in advance.

Mark