Before running the x64 installer of "MySQL ODBC connector" on "Windows Server 2008 R2" you need to download an install "Microsoft Visual C++ 2010 Redistributable Package (x64)" from http://www.microsoft.com/en-us/download/details.aspx?id=14632
If it still can't run, you try to do the following
1. remove manually the "C:\Windows\System32\msvcr100.dll" and 2. Reinstall the program mentioned above (vcredist_x64).
detail: http://bugs.mysql.com/bug.php?id=70752