We have a library of several fastener family tables. Our problem is that sometimes PDMLink dumps the entire table into a workspace when all we need is maybe one or 2 instances of the table. this is very annoying as it pulls hundreds of unneeded parts into the workspace. And, in addition, many times it shows them as changed. We're on WF3 and WC/PDMLink 8.
Are the instances verified? Are there any parameters that "change" due to relations when an instance is retrieved? Try locking them as soon as you download them to the workspace. Watch out for conflict messages on save. We have a lot of experience with this.
One thing we have done is to tell the users to "Lock" all library family table items in WS after download. This has helped a lot to prevent the behavior you describe. It has not eliminated it entirely but it has dramatically reduced it.