When doing buffered period measurements, the rate at which you can transfer data from the counter is system dependant. To try to get around this there are two things you can try. The first is to set the 'number of counts to read at a time' to a greater number. This way, the 6602 board will use less calls across the PCI bus. If possible, try to limit the number of pulses coming in on the gate that you are using to latch the counts, though in many applications this is not possible.
Make sure that you minimize the PCI bus activity on your computer. This includes, video activity and any network activity along with anything else that is connected to the PCI bus.
Brian