We have a category with around 12,000 products and when I try and save it, the page just spins for a few minutes then I get an internal server error. The errors are connection is reset or timeout errors. But I can't imagine that it should take this long to save the category.
Update to this: It seems to time out with any category we have tested so far with at least 4000 products. It doesn't even have to be a category with 4000 direct products, even a category that has sub-categories with products totaling 4000+ won't save. The default category will save though, which is odd. Has no one else had this issue?