Kevan,
The best tool Tech Support has currently to discover why something isn't working is the Support Package. These packages our users create and send into us. These can be created from the help menu/create support package. If you have a known case of something that is not being sent to the server, then it would be helpful to create a screen shot highlighting the object. The issue I am thinking of is, if you run a send and receive and another user runs a send and receive and still only you see the object, while the other user with the same layer combinations set does not see it, then that is the time to create this support package and a screen shot.
The support package is a bit of a misnomer, because it is unlikely we will be able to "support" you with it in an immediate way. The fix to your specific problem, more than likely, will only arrive in the next hotfix. Although in some cases we are able to provide important suggestions after examining its contents.
In cases like the one you mentioned, you and your teamwork colleagues should save a PLN, via the file/save as menu item. This is just a safety, in the event you need to re-share the project. The PLNs also provide a reference if certain elements need to be copy/pasted back into the teamwork project.
Re-share the project if this problem persists universally with all users. If it is only occurring with one user, then that user with the assistance of the local data manager should remove his/her local data and then reload from server.
Hope this has been helpful,
Graphisoft Technical Support