Mail Store over the 75gb limit on standard 03, cleared out junk but change in size not reflected on store

Everything works now, the problem was indeed size of data base file - both files together - priv1.edb and priv1.stm have reached 16 383 MB and I was using Exchange 2003 without SP2 (which has exactly 16 383MB as limit for data base file). I still don't understand why just before reaching this limit sending was randomized - maybe some messages were too big to pass already? Not sure.

In case somebody has a similar problem to mine, here are links with solution:

How to obtain the latest service packs for Exchange Server 2003:

support.microsoft.com/?scid=kb%3Ben-us%3B836993&x=11&y=7

Database Size Limit Configuration and Management (from 18GB up to 75GB):

http://technet.microsoft.com/en-us/library/aa998066%28EXCHG.65%29.aspx

Thank you for your answers and comments, you both helped me a lot !

That's beyond "rather high"-- that's exceedingly, mind-blowingly high. I have boxes with over double that number of mailboxes running on RAID-5 on old-as-dirt 7,200RPM Ultra160 SCSI drives with much lower disk queues.

Something else besides Exchange is thrashing your disks. I'd throw open Perfmon and graph the "IO Data Operations / sec" in the "Process" object for each individual process and see what process is causing so much IO.

Edit:

The article you linked in your comment to Jim B has some very good perfmon counters to have a look at. I'm wondering, too, if you've put a virtual memory pagefile onto those disks and are seeing excessive paging.

I do have some suspicions, after reading the article and linked articles re: Entourage that you might be having some issues associted with those clients. Outlook Anywhere (aka RPC over HTTP) isn't going to cause the same problems that Entourage will, though-- that's a different thing entirely (MAPI over HTTP, versus WebDAV which the Entourage clients use).

It goes w/o asking, but are you seeing anything odd in the event logs?

Edit after your update:

The total number of reads / writes isn't really what you're looking for. You're really looking for the delta in reads / writes on a per-interval basis. Throw open Perfmon, clear the default counters, and add some counters for:

• Object: Process - Counter: Data Operations/sec - Instance: conduit.exe
• Object: Process - Counter: Data Operations/sec - Instance: store.exe

You might also have a look at the Microsoft Exchange User Monitor (nice little article about its usage available at http://www.msexchange.org/tutorials/Microsoft-Exchange-Server-User-Monitor.html). This won't show WebDAV sessions, but it might give you some insight into what your traditional MAPI-based users are doing.