It appears that a recent update to Exchange Online has affected the ability to page a FindItem operation using an AQS String past 250 items eg http://msdn.microsoft.com/en-us/library/office/dn579420(v=exchg.150).aspx . I know that the throttle changes has limited the maximum number of items returned in one call to 250 but you should (are where) able to use Paging to the get the next 250 items for a particular query. Eg any AQS query will now only return
<m:RootFolder IndexedPagingOffset="250" TotalItemsInView="250" IncludesLastItemInRange="true"><t:Items><t:Message>
If you use small page values you can page up to 250 items but not past it. I think it also affects OnPrem 2013 SP1 CU5 it's pretty easy to reproduce.
Can somebody confirm this is a bug being looked at ?
Cheers
Glen