Thanks for the friendly reply!
So, it may be the battery, but those suckers were just charged and should last three years between charges (the last regular batteries lasted that long). You never know though! Something to eliminate...
I did some more messing around on my VCS last night and I plugged a wired keyboard into the front. Works like a charm every time. To add more information to my experimenting to get the right set up, I think the powered USB strip I have is what is doing it. It is a seven port USB strip that is plugged into the back. When the Logitech is plugged into it (or it the usb strip is plugged in at all and the dongle is just plugged into the front of the VCS), I have the issue of it barely working. When I unplug the USB strip and just plug the Logitech in, it works fine, but this defeats my purpose of having a powered strip plugged in all the time so I can hook four instruments and two wireless accessories up at once. I think the number of things plugged in and how the potential lag of the USB strip communicating with the VCS that is doing it. Additionally, the wired keyboard works perfectly with everything hooked up. I have a wired keyboard I use for my Switch, so until Atari fixes this on the backend, I should be good. PITA, but that's part of tinkering. Again I say though, this should not be activities bound to the tink list for an advertised and capable feature....