New Transmission add-on thread

Hi. I am a new owner of an Ultra and have been trying to get Transmission 2.13 to work. Here is my problem:
Before installing the add-on, I had a share named "Media" with a folder named "BitTorrent". After installing the add-on and completing one torrent download, I was unable to find the downloaded file(s). After searching the forums for some information I found that rebooting was required to see the folders etc. After rebooting, I was able to see the files in "Media/BitTorrent" but all my other folders from the share had disappeared. I found a similar issue in an older post [http://www.readynas.com/forum/viewtopic.php?f=36&t=32865&start=0]
I also noticed a separate share in the share listing named "media", which I could not see in explorer. When I uninstalled the add-on, my folders reappeared and the downloaded data disappeared. I tried renaming the share "Media" to "media" but for some reason I am unable to rename it. Re-installing the add-on once again hides all the other folders, and brings back the downloaded files.
Can someone please help?
Update:
With Transmission installed, all folders in "Media" are missing when browsing with explorer (win 7). On the other hand, if I browse using an ftp client, I can see all folders/files but not the files downloaded by transmission.
Update:
It seems that Transmission is creating a new share called "media" which is making the existing share "Media" invisible somehow. I had tried editing the "settings.json" file to change "c\media\BitTorrent" to "c\Media\BitTorrent", but after making this change, the Transmission service refused to start.