I am currently working on a 1.9 Community Magento site, right now, has nearly 50,000 products. I am utilizing the Amasty Customer Group Catalog plugin to assign a credit system to all products using a Customer Group Rule, but the Customer Group Rule caps out at 1000 products per rule, or it throws a token error.
The issue may caused by server configuration. like the default value of max_input_vars from PHP.
Try changing this value from default to something higher like 2000 and see how it goes.