My customer is having the same issue. The only thing I have found that works is rebooting the server. My guess is the Quickbooks is having a memory leak or the database has consumed all memory and it is starting to use virtual memory (using hard drive space as virtual memory - it is much slower). Rebooting will load everything fresh. This usually works for a few days. Scheduling the system to reboot overnight is the only thing that has worked so far. 
Quickbooks should move to SQL server to hold data. They cling to old proprietary technology to keep users from being able to move to another software package.