Hi Alice,
Here's an illustration of the problem:

This project has two submodules - one called hyperion-web, located in /hyperion-web, and the other called net-module, located in source/net. As you can see, the Git Repositories view shows the hyperion-web submodule but not the net-module submodule. From the left pane you can see that it does recognize it as a submodule, though. Additionally I'm able to check in changes from the Git Staging view. I'm just not able to sync changes using the Git Repository view - I have to go to the command line to do it.
I couldn't tell you how to reproduce it. Two other projects that have net-module in the same relative location are showing the submodule just fine.
Scott