I got nothing for you, C5rftw. I'd say nute stain, but the discoloration is above the water line. Overall those roots look healthy and well established like they are - or were - growing in good water conditions.
The only time I get real nervous is when I do a full reservoir change, unless I'm growing in sterile conditions (i.e. using H2O2 continuously as a preventative measure). I discuss this in detail in my response to PolishFalcon420 (Post #18 and 55) in my grow thread, but in short when you do a complete flush/clean you are also flushing the beneficial bacteria/fungi that have been helping protect your plant so it can thrive. Not only this, but you are rapidly changing the environment it is growing in - from an aged, perfectly balanced environment were everybody was working together as nature intended to an unbalanced new environment where it basically has to start over.
If an established plant growing in good water conditions is ever susceptable to attack it's when you do a full water change/cleaning in my opinion.
I'm not trying to scare anybody, this is just my opinion and I know it flies against conventional wisdom. There is probably a simple explaination for the discoloration. I am almost certain there is nothing wrong with your plants C5rftw. All I'm saying is to keep an eye on both the plants and roots. If the plants start to wilt when they haven't before, or if the discoloration continues or spreads for no apparent reason, or the roots get a slimey substace on them, or the water starts to foam or smell, then I would take some kind of action.
Just my humble opinion...