There are a few reasons for this behaviour as detailed below:

1)    Indexing engine shutdown
If the indexing engine shuts down while data is being sent to it, it can cause a situation where Enterprise Vault believes the items have been received (because no error was received) but the indexing engine did not receive the entire batch (and so does not process it).
Enterprise Vault waits for the indexing engine to generate acknowledgements for these items that never arrive.

2)    Indexing service stops processing an index volume abruptly
If Enterprise Vault stops processing an index volume abruptly, for example to enter backup mode or subtask is stopped, then if any error reported by the indexing engine for this index volume related to the data sent can be missed.
This results in Enterprise Vault waiting for the indexing engine to generate acknowledgements for these items that never arrive.

3)    Complex message encountered (timeout)
If Enterprise Vault sends a complex message (e.g. large expanded distribution list) that requires a lot of processing as it is being received) by the indexing engine (within IIS), it can take too long to send. There is a timeout (in IIS) of 30 minutes (by default) to send a ‘batch’ of items to the indexing engine. If this timeout is exceeded the indexing engine fails to process the item but Enterprise Vault waits for acknowledgements for these items that never arrive.