I don't have an answer for you but from the TPI swappers guide book that I have the vss is said to control the torque converter lock up, controls the idle circuit, controls carbon canister purge, and the mph fuel shut off. Maybe the last one could explain your problem. Since fuel injection fuel systems are pressurized the moment you lose pressure to the system your engine should stall unlike a carb. Don't know if that scenario and the vss would be related in your case but it could be a start if it is not the timing.
I wish I could be more help but I have not messed with a tpi firsthand yet. Just waiting to get my hot rod built so that I can get started on my 72 Chevelle tpi twin turbo build. By that time I should know more but that is a long way off
Good luck and hopefully someone that knows firsthand what they are talking about will chime in.