How many workstations DO you have?
What/how is the database being used?
Are you sure all the duplex settings on switches correct (i.e. full duplex on Gigabit is a given; does the 100 Meg setting match the workstation settings).
When running “off hours” from a workstation on the primary gigabit switch, do you get similar response times, or is it vastly improved?
If you have problems with this equipment accessing the application, you may run into problems with file/record locking and application design, more than the network as you’ve described.