My guitar teacher taught me the best way to coil the cables for electric guitar and amplifier cables (any tear in the inner copper wiring can create artifacts in the sound) so i use it all the time now, on any type of cable.
For starters I need to point out that any wire has a natural resting position, colied at a specific arc. That's because the materials used in them have a resistance against being bent (kind of like a spring, or car tire if pressed while sitting upwards).
Your goal is to wind the wire so that the actual coil is not too tight and strain the isolation or the inside conductor wire.
The PS2 has a really small radius around the middle and most probably, you force it to that radius and bend it to an arc that is smaller than optimal until the rubber gets old and eventually gets cut via strain.
Also you need to be careful not to twist the cable around it's axis. Inside, the conductive wiring is fairly sensitive even if the material is flexible.
That being said, let's wind the cable:
- Cable wire in one hand (preferably close to one end) and wire (at a resonable distance from hand A, you'll see why) in the other hand (let's call them hand A and B)
- Start twisting the cable gently with the tips of your fingers in hand B while holding the other end in hand A. Notice the cable producing a slight coil according to your twisting motion and that the cable "wants" to get closer to the point you hold the cable in hand A. Don't force the cable into the hand A. You need to find it's natural resting arc.
- The wire will coil itself and produce a round circle, the coil, that you can hold with hand A. Now you have one coil that is held by hand A while hand B has more wire to wind. The size of the coils should vary depending on the thickness of the cables.
- Keep doing it until you have a neat bundle of coils that you hold in hand A.
- Provided you've wound it nicely, you should not feel a big resistance at the middle of the coil bundle if you'd be to tie them together with a piece of wire right in the middle part, so that you flatten the coils into a ribbon like bundle. Alternately, only tie one side of the coil bundle, but the coils might fall apart and unwind and you'd have to do it again.
As far as controllers go, never coil the wire on the controller, it's too tight and it's always straining them, hence the problems.
Also, don't coil the wires on the analog sticks. Their springs aren't supposed to resist a wire wound around them.
You can coil it this way that I just explained "around" the PS2 controller, just keep in mind, you can't wind the part that goes into the controller, it may break because of the way the wire is inserted into the plastic case.
In my experience, the controller cables are annoying, but coiling them ON the actual device is always problematic. I'd say keep them under the actual controller with the tying knot on only one coil side.
Keep in mind, never strain the wires, they know what they want.
I am sorry, I cannot provide any photos at this time and I hope this was descriptive enough.
When Microsoft releases firmware updates, these updates occasionally include improvements for your controllers. Unlike the Xbox One updates, which are applied automatically, controllers need to be updated manually. Headsets too are often updated so keep them plugged into the controller while you update. Here's a paragraph from the Microsoft Xbox One website about the controller update procedure. Follow this and see if it solves your problem:
To download the update, connect a controller to your Xbox One with a
USB cable. Keep any headsets connected to the controller. Connect to
Xbox Live. Press the Menu. Go to Settings > Devices & accessories and
select the controller. If you have multiple controllers attached, you
can select Buzz – which will cause the selected controller to vibrate.
Then select Update to download the new firmware to the controller
attached via the USB cable, and the screen will show the “Updating
controller…” progress screen. When you see the “Controller updated”
screen, press B to go back to the Devices & accessories main page.
Reselect the controller.
Best Answer
To be honest, I really think it's a combination of overuse of your thumbs (~an hour) and the unfamiliar controller that's doing you in, causing "Gamer's Thumb". You said that you used Playstation controllers before, with no issue. Playstation controllers are a fair bit smaller, and a bit different in terms of layout compared to Xbox controllers (namely the left thumbstick and D-pad are switched).
This would probably cause discomfort after a while, as you're not as familiar with this controller as you are with a PS controller. So, like in this post, give it a break, then come back to it after a while.