I'm pretty certain that this tuning issue is on the JTV side of things. I've done much with all this gear I can't speak about publicly, but after all the trials, the issues of tuning lie with the JTV 99.9% of the time in my experience.
Have you tried stepping back onto the TapTempo/Tuner FS instead of going direct to a patch? If so, does this same glitch occur? If not tried, perhaps try that and see if it still has the same issue with switching to standard.
Also as I've read on your post, you play 1/2 step down. I would suggest physically tuning the guitar the 1/2 step and save yourself one problem at least. Plus for any dual patches like combining mags & Models, you'd need to do that anyway. All tunings from the physical string tuning is what the guitar generates. The JTV guitar does not "know" if your strings are tuned to (440) standard, or any other tuning. All alternate tuning is based off of the physical tuning of your guitar.
For example - the "standard" tuning slot on the alt tuning knob is not literally (440) standard tuning.
It is just one way of "forcing" the guitar to play what the strings are physically tuned to if you had a patch with a Workbench created or Dynamically created alternate tuning and you wanted or needed to go to your strings physical tuning for any reason and not simply shut off the modeling by going direct to mags.
This would accomplish the same thing, but what if your patch was an acoustic guitar of some kind (and all was working properly with alternate tunings like in JTV 1.71), or a Sitar, or a Banjo - that wouldn't work would it? So the engineers thought to add this "seemingly useless feature" on the alt tuning knob for just such an occasion.
You have a model in an alternate tuning, and you want to keep that guitar sound, but need the tuning to be standard - there it is on the guitar. You also cannot store dynamically created alternate tunings to that slot either...probably for the same reason the engineers originally decided upon.
Hope this adds soe more light to why the guitar does what it does when all is working correctly.
PS - my HD500 just blew up and I'm 100% screwed unless I can get someone to help me fix the problem before my gigs that start Thursday thru Sunday!! Aaaaaaaggggghhhhh!!!!