First, I hid the 'my computer' node via the filter/node options.
I have recently been ripping a bunch of cds again, and was pleasantly surprised to find that the cd's show up on the main node when the my computer node is hidden. When the cd is removed, so does the icon on the main tree.
The problem seems to be, that when cd is removed, viewable/scrollable tree window is reduced.
I suspect this is happening because when the drive icon is removed from the tree node, the scrollbar size changes.
After cycling through several discs, you can no longer scroll to the bottom of the tree (the scrollbar is at the bottom of its travel) and unable to view or navigate to nodes there.
Here is a series of screenshots to illustrate the problem, as you can see the cd is displayed in the main tree node (because my computer node is disabled). This is actually a great hidden feature, please do not change it.

Ok in this next one you can see that the last node is right at the bottom of the scrollable tree window.

and now, I have removed and re-inserted the cd, and now the 'classification changer' node is no longer visable or scrollable to.

And finally, removing the cd once again, causes both the cd and the upnp server node to become unable to be viewed due to the scrollable view reduced.

This is all completely reproducable, but I think it is also specificly dependant to having custom user nodes on the main tree, I have not tested without any scripts.
It should also be noted, that the missing nodes are still there and accessible via keyboard control or activating a node via script, however the node still remains out of the viewable/scrollable area and thus is hidden out of site within the tree node itself (the applicable track view for a particular node is still correct).