Bone rigs not mirroring correctly

So i have no clue if this is a bug or not but i am guessing it is since its affecting literally every rig i open in blender.
The current issue i am having is all the rigs i open up in blender, including mine, have their bone roll axis mirrored incorrectly with the x axis pointing the opposite way the left hand side is ponting, and no matter how many times i have tried to fix it by following all other videos and forums instructions, i have had no luck.

The strangest thing is that on one of my models this problem only affects the upper half of the rig while the bottom half has no issue whatsoever and i have no clue what caused this to happen but i will leave the link here so you can see for yourself:!5sIGFbKJ!_MwpY9d-cm1clv6v2im27xR1lYPwdNk8-ISdd17Hgu8

Another problem i am also having and suspect might tie in with the problem is after using the correct naming convention for left and right, the flip names function fails to flip the names correctly giving me results such as “UpperArm.R.001”
I have tried:

Recalculating the bone roll straight after applying all my location, rotation and scale data.
Reinstalling blender
Using symmetrize to mirror my rig but still ending up with the same result
Remaking one of my entire rigs from scratch following tutorials online to the letter
Using the x-axis mirror and using ctrl-r to roll the bones into place
I have tried mimicking the problem on a small scale by making 2 horizontal bones and mirroring them while trying every fix on the internet to get it to work. I have no clue anymore if its my fault or the software 's. Any help is appreciated, thank you before hand.

I briefly looked at your blend. I don’t see the issue. Perhaps you can simplify it for me. What exactly are you doing and what exactly are you expecting? On the issue of Flipping names. the .001 is added when it already has a bone named the same.
Set your Pivot to medium. You have it set on cursor now. If you want, just send me a PM. I sense great frustration.