Hi there,
Are you modifying the items through CIFS?
With earlier versions of Alfresco, including Alfresco 2.1, we hadn't consolidated the code behind the various interfaces into the AVM. When you accessed your sandbox via CIFS, for example, you were going through a code path which was significantly different than the code path used if you were to, say, upload through the web client.
As WCM has matured, we've focused on establishing a WCM Services layer (Java and REST) which the entire product is steadily becoming more reliant upon. This is especially important for Alfresco 3.1 and beyond.
While I can't say definitively what the story is with this problem, I would recommend that you consider upgrading to a newer version of Alfresco. In particular, we've recently released Alfresco 2.1.7 (for the 2.1 family) and we're about to release Alfresco 2.2.3 and 3.1. These all build upon some improvements to the underlying handling of modified items. It may have an impact on your issue though I'd recommend that you check with support to be sure.
Michael