Currently, there is a limit as to how many feeds each user can have in their reader. That limit is set at 1000 feeds. As we gradually grow in both our user-base and our internal infrastructure, we may expand that limit to more than 1000. However, as things stand now we will not be able to load more than 1000 feeds into your reader.
If you have under 1000 feeds and the problem persists, please contact support.