In running the 4.1.3 DST agents I discovered that the getallentriesbykey method that they use was only occasionally capturing all the documents that it was supposed to. It would always work on the first mail file specified in the text file but subsequent to that it was VERY spotty on what it would find.
It seems to work fine with no error but the document counts in the logs are very low. I have validated this behavior from both the client and as a background task on the server. Each time you run the agent it finds a different subset of documents.
The resolution that I came up with was to run the agent one time for every mail file by having another agent call the main one.
HTH
Rob