I tested brainalinger on windows yesterday, it works fine!
Although I also got "Fail instantiation" errors as you listed above, but they are not about brainaligner and seems they will not effect it. 

Since the program complains it can not find your images, maybe you can try to use the absolute path instead, below is paras I used. Hope this helps!

#global alignment
.\vaa3d_msvc.exe /x brainaligner /f brainaligner /p "#t d:\downsampled\mouse17545redl5_s2.v3draw #s d:\downsampled\mouse17302l5_s2.v3draw #w 0 #o d:\downsampled\mouse17302l5_s2_jba_global.tif"

#local alignment
.\vaa3d_msvc.exe /x brainaligner /f brainaligner /p "#t d:\downsampled\mouse17545redl5_s2.v3draw #s d:\downsampled\mouse17302l5_s2_jba_global.tif #w 10 #o d:\downsampled\mouse17302l5_s2_jba_local.tif"


-Lei