mslina2002 - 4:25 am on Aug 23, 2012 (gmt 0)

june 23-25th saw a 20,000 peson loss,

Yep, you have been hit with the Pandasitus 2.8
That came out June 25.

Our site is Q&A, in a specialised field. We use our own custom software, it's similar to stack.

So it sounds like you have lots of UGC so have you checked some of those pages that have a question posted, but no answers given? Likely candidate for thin content there.

What about user registration pages? Are the noindex, followed or do you allow members to have their pages indexed?

From what you describe, your site reminds me a little of the daniweb site which is also Q&A type format so you could read up about her site: [webmasterworld.com...] where apparently she recovered from Panda.

However I just had a look seem traffic is gone a bit down since a few months ago.