Sgt_Kickaxe - 3:06 am on Jul 26, 2010 (gmt 0)
On site we have made lots of changes.
1. On 18th June i made thousands of inner pages noindex.
I think you've outlined the likely reason already and if that's not it you won't know it until these changes propagate fully which can take months.
In the mean time I'd suggest not making more changes until at least a couple of weeks go by, a couple of months if you can wait. When the dust settles you can evaluate your previous changes and either make more or undo the ones you know didn't help.