Seconded! I was using my Saitek X-56 in 1.3 (I think? It may have been an earlier version, all I know is it stopped working somewhere around this version) quite happily, having plenty of toggles and buttons to use for all of my action groups with some left over besides. But then one day it started doing exactly what the OP described: when it worked all the joystick keybinds would say something like "joystick0button1" clearly identifying the joystick (well, maybe not clearly...but you know what I mean.) but now it just says "button1", and since the X-56 is two separate devices, one throttle and one stick, they both have a button 1 on them. So, for instance, I have my staging button set to the main stick trigger, which is Button 0 in this game. And then I have the Brake action group bound to the thumb button on the throttle (which is a separate device), but it is also labelled as Button 0 in the game. So then whenever I press the staging button trigger, the brakes activate. Whenever I activate the brakes, it stages as well! But wait, there's more!
I tried using vjoy and universal remapper (can't remember the name, it's 3 letter acronym like UKR I think? I dunno.) to combine the inputs into one virtual device so the buttons wouldn't conflict. Sounds like a great idea, right? Yeah, I thought so too... but in reality, while it did fix the duplicate mapping issue, it created a whole new problem: the game would register inputs from both the virtual device AND the hardware device at the same time. So, again let's say I press the trigger, which is Button 0 on the hardware device, and it is remapped to Button 4 in the virtual device. Any action bound to either Button 0 OR Button 4 will activate simultaneously when I press the trigger. I tried several different variations on mapping, like setting vJoy to have 64 buttons instead of 22, and starting the remapping process from Button 64 instead of 1. Well, apparently either windows or the game itself cannot handle more than 32 buttons on a device, so that didn't work. And when I set it to 32, it stopped recognizing the virtual device altogether, so I just gave up and dusted off my old Thrustmaster T-Flight HOTAS X for this game, which works fine, though it doesn't have all the functions that I prefer like the X-56 (The mini-thumbsticks are superb for translation!) at least it works properly.
The only thing I discovered that may or may not be important to this issue is this: when I was setting the bindings, I actually got it to register as "joystick0button0" like it used to by pressing both of the same-named buttons at the same time; so if I hold the trigger (button 0) on the stick and THEN press the thumb button (also button 0) on the throttle, then it would register as joystick1button0 in the bindings. However, when I tested this binding in the game, I had to do the same thing in-game to get it to register, meaning I had to hold the trigger and then press the thumb button on the throttle to activate that keybind. I wouldn't recognize it otherwise. I surmise it must have something to do with some sort of dynamic input api in the game or maybe in steam that is trying to manage input devices on the fly, but apparently it has some sort of bug that de-registers any device that doesn't currently have an active input or something. That's just a wild guess though, I honestly have no idea. But yeah, I really enjoy having a HOTAS system for this game, even though it isn't really the type of game most people would think of using a HOTAS for. It is no Elite Dangerous, in other words but still, it makes things like rendezvous and docking and especially precise throttle control a LOT easier. I can get MechJeb-like precision executing maneuvers without MechJeb. And besides, the experience just feels better when you have your hands on a real joystick while controlling a spaceship! So, yeah, I guess it's bug report time because I'm out of ideas on this one.