Blackra1n by GoeHotz is a 2 minute jailbreak utility but it doesn’t adds the afc2 support to your jailbreaked iPhone. iPhone browser, iFunbox, Diskaid etc uses the afc2 service to access the file system and allow the transfer of files such as Winterboard themes, NES ROMs or eBooks to the iPhone. In short you can’t access root partition of your drive with desktop clients. GeoHotz also tweeted that he disabled it because of issues whilst making the JB but said look arround cydia for a fix.
And here is Cydia fix released just some hours ago, afc2add solves all your problems with iFunBox, iPhoneBrowser, Winterboard, SBSettings and all similar applications with blackra1n jailbreaked iPhones.. Just open the cydia and search for afc2add and install this patch. After installation reboot your phone and you’ll be fine again.