I personally have never experienced this issue, and I've run tests with 200, 500, and 1000 players. So I can't say if it's a PC speed issue, memory issue, or an Internet Explorer issue.
Frankly, I would hesitate to run a tournament of that size with full player tracking using any software. You're going to spend your entire time busting players out and moving them. Tournaments of that size usually have several tournament directors managing player movement, etc.
I would put the software in Simple mode (Players tab -> Track Players button) and run it that way, and get some help in balancing tables.