Hi ssidle,
You're right. We did additional testing and the problem is syncronization, not intentional 'hiding' of 'system'directories and files. Also it did first appear in 3.3.4.
The 3.3.5 upgrade DID NOT fix it.
In addition to not synchronizing the directories (showing them), it sometimes does not remove entries in the file manager for files/directories that have been removed. We even just used file manager to rename a file (the aspnet.gif that comes with the portal). The new name showed up, but the old name was NOT removed from the file manager listing. No amount of syncronization could fix it.
We did load and delete some skins to do additional testing through a module. Fortuneately, the module can see the new skin directories and files. Unfortunately, the file manager cannot. We were able to synch the directories by clicking on the 'skins' folder and selecting the recursive sync. However, the file manager DID NOT remove the old directories from the skins that we uninstalled.
The bottom line, is that we (and I assume a lot of others) are hobbling along. We had upraded to 3.3.4 because of urging by the core team. 3.3.4 fix a security hole in 3.3.3.
Now that most of our sites have migrated to 3.3.4, we have to manually do a lot more than before.
I can only hope that the Core Team is fervently working on this problem (I checked Gemini, but nothing in the PUBLIC bug tracker). A problem like this shakes our faith in the platform a bit. We have been VERY happy with DNN, but a mistake like this is tough to excuse.
Hang in there and good luck!!