I can confirm I am not using any third party input tools. I use a cheap "pro pedal" i got off amazon for my rudder pedals, a T16000m thrustmaster for my stick, and the accompanying thrustmaster throttle. I have as a result 3 inputs for my rudder, but my twist is broken on my joystick so that's disabled, and i don't use the rudder pedal things on my throttle (which are by default in a neutral position) so that's also disabled.
I would be glad to post the track file, I found it, but it is a little long. How would I go about cutting the file so you don't have to sit through like 40 minutes of nothing?
To mention to @BIGNEWYas well since you mentioned it. I also haven't been able to replicate this. This was a one time problem that appeared during this flight and since I haven't had any rudder malfunctions. It's why I think this may have been some sort of rare bug or something.
In any case, if anybody would be so kind as to tell me how to cut down my track file, I'd gladly provide you with it.
Edit for extra information: I do use a third party software, but the only one I use is SRS, the radio tool. So I don't think that should interfere with this. That is as it stands the only third party software I run in DCS as it stands. (unless you want to consider plane skins third party software, but even then I don't have many.)