What kind of hardware are you running PrintShop Mail Web on? If you have 600 clients that often create orders (which implies softproof creation, generating output print jobs, traffic on the network and a lot of read/write on the disk), it may simply be that the server lacks the power necessary to make complex queries easily.

Edit: What do you mean by FTP accounts? PrintShop Mail Web doesn't have FTP capabilities, so how are you implementing the creation of FTP users, and how exactly are they submitting jobs? Seems to me like a very non-standard way of using this system...

Edited by Eric Lachance (12/15/10 12:49 PM)
Edit Reason: question on FTP