The MSDNAA Downloader is not good at all. I have wasted well over 20Gb of bandwidth trying the download from different computers and different networks, having to ask for my download limit to be raised more than once (it takes them days to reply). The checksum it does is completely useless, it will happily give you an empty file and say it's ok. You must run a checksum yourself and compare against the values listed here:
http://slickdeals.net/forums/showthread.php?t=1559001
In case that page goes down at some point in time and someone ends up in this post and wants the checksums, I copy them here:
eng_windows_server_2008_r2_st_ent_dc_web_retail_x64_X15-50365.img
2996783104 bytes
CRC32: 8F94460B
MD5: 0FFBAE83327F0AD8C2AB4D5DFA754C09
SHA1: A548D6743129F2A02C907D2758773A1F6BB1BCD7
SHA256: 4c6604cde90a7c44b3cc990884b1fd428883281d0dfbf4e55f6a9f82a1092a6f
The way I finally got it working was using dreamspark.com to download from the web (not the Downloader) using Google Chrome. Install worked using Windows 7 (64-bit) in Virtualbox.