Have you changed any cache settings? If your server is caching responses when we attempt to crawl it, we won't see the new feed. We also rely on the etag or last published date headers to determine fi the feed is outdated. If those aren't being updated correctly then we won't know the feed was updated. Just a couple of things to check.
Although, we don't check the headers when you manually refresh the feed so I would look at any server caching first.
Do you get an error at all when you attempt to refresh manually?