Which version of WiX are you running? There was a bug a ways back about that.
> From: mathew.skil...@aspect.com
> To: wix-users@lists.sourceforge.net
> Date: Tue, 27 Aug 2013 14:54:30 +0000
> Subject: [WiX-users] 64 bit version of MS build cannot find the WIX toolset
>
> I know there is probably a posting somewhere out on the web describing the
> issue I am having, but I am not able to find it at the present moment.
>
> The problem I am current having is that the 64 bit version of MS build does
> not properly evaluate the build variables and is not able to find WIX tools.
> The 32 bit version works correctly and everything is happy, but when I switch
> MS Build targets everything goes to pot.
>
> Does anyone have a way around this issue or a link to the documentation on
> why I am seeing this?
>
> Thank you in advance,
>
> Mat Skildum
>
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