Replace the battery, make sure the Vapor is getting power from a source that only gets power after the ignition is switched to on. Otherwise, the backlight will not turn off. It won't kill your battery, but I tend to think it draws unnecessary attention to your bike when parked at night.
If you run on the Vapor's battery alone, the backlight turns off after 10 min or so. This is annoying when riding at night.
Vapors usually hold on to their settings even when the battery dies. I had to replace my battery many times, but don't remember ever having to redo the settings.
I think there's a factory reset button on the back. You may want to try a factory reset, then redo all the settings. Then see if that does anything.
There's not much to do as far as adjusting the magnet & pick up. If the magnet goes past the pickup appropriately, there's not much else to do. There's not more than one magnet on your brake rotor or wherever it is you attached the magnet, is there? Maybe check that?
If all that fails, seriously, call their customer support. They're not a huge outfit. I don't think it's very difficult to get ahold of a human being. They can help you troubleshoot. Plus, if the unit is defective, they probably won't send you a new one for free (although they did for me once), but there's a chance they will offer you a head unit at discount). At the VERY least, they'll let you order a replacement head unit (which is a discount from their kits because it won't include the sensors, wires, etc).
Update: I am going to keep the Vapor (for now) I got everything set except the speedometer is still reading wrong. It keeps telling me that I'm cruising at ~450mph and pass people doing ~564

I altered the wheel size in the settings and it keeps reverting back to the previous setting. It's on wired power not battery so I might change the battery and see if that fixes the issue. If that fails, Ill have to adjust the magnet/pickup. If all fails, ill just have the caged wife next to me on the freeway and mark the conversion and just run with it.