Wix# provides a significantly reworked API around building MSI, however for building bootstrapper the interface is almost identical to WiX. Thus Wix# becomes just a convenient candle/light launcher. Meaning that if you could do this with WiX then you definitely should be able to do this with Wix#.
In the situations like yours I usually use Wix# to produce the WiX sources and the conduct the actual troubleshooting on WiX (source + tools).
I suggest you change your build script to call BuildCmd instead of Build:
This will result in the creation of the setup.wxs file (instead of *.exe) and the batch file Build_setup.cmd with the all required commands for WiX tools being properly prepared.
From that moment you can forget about Wix# and treat it as a canonical WiX build that is misbehaving. This way it will become obvious if there is something wrong with Wix#, WiX or the setup definitions (C# or WXS sources)
In the situations like yours I usually use Wix# to produce the WiX sources and the conduct the actual troubleshooting on WiX (source + tools).
I suggest you change your build script to call BuildCmd instead of Build:
var batchFile = bootstrapper.BuildCmd();From that moment you can forget about Wix# and treat it as a canonical WiX build that is misbehaving. This way it will become obvious if there is something wrong with Wix#, WiX or the setup definitions (C# or WXS sources)