This may happen because your transport service has stopped polling the expander because the polling / maximum polling time intervals that are configured in the Transport service configuration file reach their limits. Assuming this is the case, Deployer continues to deploy the files, but the Transport service refused the check. However, I expect that the status message will ultimately fail in the publish queue.
It is unclear whether you are using GA or SP1 for SDL Tridion 2011. There are a number of hot fixes to help resolve these issues for GA and HR1, all of which are included in Service Pack 1 (SP1). In particular, they solve some problems associated with returning responses to the transport service after some (non-catastrophic) failure in Deployer after it receives a large queue of elements or a large transaction that has to be dealt with. I highly recommend you install the latest fixes before attempting to customize behavior through configuration.
If you have already applied all the corrections, check if you applied them correctly (copied all new banks, etc.) to the CD side (Deployer, Broker, etc.), as well as to the CM side.