Chenyang,
I was able to get it running on Server 2012 R2 as well.
Couple of things I noticed during my install attempts:
1. Make sure that you are using the keys.ini from your other server so that you can properly decrypt the passwords for SQL Server access.
2. Make sure you're using 64 bit Java, which it looks like you're doing. You're a IDM'er after my own heart, keeping to version 6. My VM has patch 41. You might want to try that. When you're setting up your connections use the OLE for SQL Server driver.
Hope this helps!
Matt