I think that you're running into a limitation of the counter itself. My manual for the 53131 says that it can can do a maximum of 200 GPIB measurements per second. I think that the 53132 is similar except for extended resolution. What you might try is the STATS mode where you command the counter to take a number of measurements and then calculate the statistic. It is generally fster to let an instrument do a series of measurements and accumulate the results than to try and transfer one measurement at a time over the GPIB bus. VXI, PCI, PXI instruments can do things a lot faster so that might be an option as well. You should also be aware that your rate of 10 kHz requires timing resolution greater than what is in a PC (a PC has 1 msec resolution at best a
nd it's not deterministic at all) so if you need something accurate, you'll have to use external hardware timing.