The idea when we wrote the system was that it was supposed to be used for handpicking, and we didn't see that anyone would use it for thousands of caches. Therefore, we made a limit of max 5000 caches (or is it 10000?). However, we know there is some bug with that limit and it is possible to add caches regardless of that limit in some cases. We have not investigated this since we are working on a complete rewrite.
This is not your problem though. But the problem with big lists are that they get very heavy for your computer. 5000 caches is usually not a problem, 10000 caches needs a browser with fast JS-engine (firefox is pretty fast) and a fast CPU.
The plan with the next version of VGPS is that it will be faster and that it should be technically possible to handle 10000 caches without a problem.
Until then, the only thing we can do is to tell you that better browser/hardware might help, alternatively, we can help you remove the VGPS itself.
Version 2 of VGPS was planned to be released this year. But changes in the tax systems within EU we have had to stop that the VGPS work and focus on this instead, due to the very hard deadline.
Also, I must admit that there is a chance that our VGPS 2 plans won't work as expected. If so, it may end up with nothing, or that we have to start over with some other technology again. It is too early to say, but we have done some tests, and we still believe in the result.