should not the 64bit build flag be "vcvarsall amd64" ?
ref -> http://msdn.microsoft.com/en-us/library/x4d2c09s.aspx

not sure what it means but i got link warning with the subsystem 5.1 flag. it did work with 5.02 or 6.00 (im on windows 8.1)
LINK : warning LNK4010: invalid subsystem version number 5.01; default subsystem version assumed
ref -> http://msdn.microsoft.com/en-us/library/fcc1zstk.aspx

Looks like you could use amd64 or x64.

Here's an excerpt from the vcvarsall.bat:
if /i %1 == amd64 goto amd64
if /i %1 == x64 goto amd64

So as you can see both options go to the same spot.

I also was getting the same warning with the windows,5.1 set in build.bat. The article msdn.microsoft.com/en-us/library/fcc1zstk.aspx (the one you mentioned) after some closer examination shows to use:
5.01 for 32 bit
5.02 for 64 bit

The odd thing is it looks like you can use 5.1 or 5.2 to mean the same thing.

So if you want to clear that warning you need to run from a command prompt that has run vcvarsall.bat x86