Firmware upgrades can break lots of settings for the media server, since the two are very badly integrated.
You might benefit from reading this FAQ:
Firstly, I’d check that both media serving settings are correct (see Q. How do I start the Twonky Media Server?).
The MyCloud media scan and the twonky media server scan are two different things; the latter is usually pretty quick (mine takes about 15 minutes for 65k tracks. If the twonky ui is reporting that it is still scanning, I’d start to think about corrupt format files.
