On a recent site, there were many issues sequencing an application. The App-V v5 sequencer kept crashing. (might be due to it needing , or requesting a reboot)
Tried sequencing the outsourced MSI, the tidied MSI, and the original EXE file. (yep, 3 sources) all ways the same result.
Sequencer always crashed.
We tried quite a few approaches to this, different approaches to the reboot, running the app, not running the apps.
Walking home I had an idea..

Sequence this in app-v 4.6 then convert to app-v v5. It nearly worked, I only had a Win7 x86 App-v 4.6 machine.
It worked better, but didn't quite work fully (we are currently doing Win 8.1 x64).

Final plan
Seq on Win8.1 x64, with App-V 4.6
Convert 4.6 sft to .appv

Successful conversion, we have an app-V v5 app!!...

 I have had to do this a few times, probably 4 or 5 times, not a huge amount, but I have definitely done it. It might be useful idea to keep tucked away in your tool box of fall back plans.