We know proto-2 engines require a good battery (or BCR) to get out of neutral, Since that doesn't seem to be a problem perhaps it's the sound file??? I could live with it just the way it is.
This is an astute work-around. Yes, as suggested perhaps try re-loading the soundset. But I suspect you don't have a TIU if you're running conventional.
The purpose of the battery/BCR is many-fold. But in conventional operation, if you can cycle thru the neutral, forward, and reverse then perhaps that's good enough? The battery/BCR is also needed to save any changes to conventional modes of operation such as locking the engine into fwd, rev, or neutral. Or remember a change to speed control on-or-off between operating sessions.
I suppose if you were really curious, you could try placing the engine into direction lock or toggling the speed control enable/disable to see if the engine retains the changed mode between power cycles. This remembering is performed after the shutdown sound completes which is of course the matter at hand since your shutdown sound stutters and flakes out after a few seconds.
If the engine does not remember a change to direction lock or speed control between power cycles in conventional, then there could well be an issue with the battery circuit. But if it does remember a change in mode, then I'm voting for re-loading the soundset...or live with it just the way it is.