Alright, i've done some more research into this problem. It seems that certain people not only have this problem wtih VBA Link, but with every other Visualboy Advance emulator. I've found numberous solutions to the problem, so i'll list them all here, you'll just have to try each one out as each one worked for someone in the world:
[*]Update your Sound and Video Drivers, as they normally cause freezing problems. Also make sure your Windows Patches and DirectX versions are up to date.
[*]Scan your computer for adware and spyware. Also check if any Virus scanners are running, and if so, try turning them off.
[*]Check if you have any driver/resource conflicts. If your sound and controller drivers or any other driver are clashing with each other, your emulator will freeze up extremely fast. Check to see if there are any other programs running that could be causing the problem.
[*]Try opening the ROM in fullscreen, then changing it back to the size you want after a few minutes.
This is most likely a driver problem so check to see that they're all updated. Good luck ;)