I have recently been battling running a command line tool within a Wix 3.6 installer. I eventually got it going but learnt a few things. Here is a code fragment that outlines the solution.

<Product ………>
……… loads of other Wix bits

  <!—Next we define the actual CustomAction that does the work. This needs to be deferred (until after the files are installed) and set to not be impersonated
          so runs as the same elevated account as the rest of the MSIExec actions. (assuming your command line tool needs admin rights –>
  <CustomAction Id=“SilentLaunch” BinaryKey=“WixCA”  DllEntry=“CAQuietExec” Execute=“deferred” Return=“check” Impersonate=“no” />
  <!—Finally we set where in the install sequence the CustomActions and that they are only called on a new install
          Note that we don’t tidy up the actions of this command line tool on a de-install –>
   NOT Installed
   NOT Installed


So the usual set of non-obvious Wix steps, but we got there in the end