I can't help you with that freaky software stuff, but the AXI Timer can function as an up counter or a down counter. The value you load into it, as well as the expected response time, really depend on which way the counter is counting.
If you want a timeout to occur in ~1 second, and your time base is 83.333 MHz, you need to load the counter with +83,333,333 or -83,333,333--depending on the direction of timer count. Your formula, above, implies you're expecting an up counter. You need to confirm that that's how the time is counting. (Check the timer control/status register--TCSRn.)