The blackening comes from either the rubber seals, reservoir hose and the plastic brake lines. It's common. It happens to my clutch fluid but not to either of the brake fluids.

 

The darkening of the brake fluid is normal.
Just change it and move on.

 

it happens within 1,000km of new fluid. i don't wish to change my fluid every 1000km. I find it funny how this is just normal on a ducati

 

Flush the fluid at least every riding season. Sooner if it is degrading enough to look black. What kind of fluid are you using? Perhaps a racing grade fluid like Motul RBF 600 would be in order.

 

not 100% sure on the fluid, i know it's motul but unsure which type. Will go for the 600 stuff this time

 

Yeah get yourself 500ml of the cheapest Dot 4 fluid you can find and draw the whole lot through the front brakes to help get all the crap out, just throw away whatever comes out.

Start by emptying the master cylinder (kitchen paper towels if you don't have a suction pump) and give it, and the rubber seal, a good clean. Then draw through your cheap fluid through both lines, one at a time.

Once you've done the above, flush once with a decent fluid and then bleed.

It's worrying that your brakes went off after a 1500Km trip, was it all in the twisties or mountains requiring a lot of braking?

If you can elevate the front wheel see how much brake lever pressure you need to apply before the brakes start biting the disks, if you have good pads.

 

A lot of the newer bikes does this, especially in the rear, cant answer why, but its what they all look like.
If it was just on Panis Id be damn sure its the little lefthanded-belt-lover-dwarf putting black pigment in there, but Multis are just the same so I have to reconsider that theory...

 

On my 996 the clutch fluid turns black pretty quick, but the front and rear brake fluid stays normal color. Gotta be leaching something out of the rubber on the inside of the cap...

 

In my experience it's microscopic particles of rubber from the master cylinders.
As Tom Tom says, it happens worse during the initial break-in period on the later bikes.
I had it with my SFS and 1199. It does get better with age on the systems.

The OP has clearly left the brake fluid in too long anyway.
At 4000 kms or more it will be looking pretty dirty, and way overdue to be changed in order to optimise the system and maintain a clean appearance.

I personally use AP Racing Dot 5.1 Brake Fluid with quite a long life before needing to change the fluid.
At the end of the day, the more one uses their brakes/clutch the more frequent the changes will need to be.

As I said in my earlier post.
Change it and move on.

It never hurts to have fresh/clean brake fluid.
If the OP couldn't be bothered, then he has 2 clear choices.
1. Is to suck it up, and get with the program then change the fluid when it gets dirty.
2. Is get rid of the bike, because the phenomenon is completely normal.

 

Did we ever reach a consensus on what the source of this problem was? I flush the brakes and clutch systems before each riding season, and typically ride between 400-700 miles over the course of the late spring/summer/fall.

I have the same issue as WideWalker... front and rear brakes are just as clean as the day I changed the fluid. Clutch fluid however is now dark gray. There is no degradation in clutch performance, but truth be told, I would rather figure out the problem and make any required changes. The only thing I've done different this year was run a Valvoline 3/4 synthetic in the brakes and clutch. The seal in the reservoir cap is smooth and clean and shows no evidence of leaching material into the fluid. Am wondering if it could be any of the seals/gaskets in the master?

All the lines and masters are the stock equipment that came with the '02 748R. Any ideas other than to change the fluid and learn to live with it?

 

I installed a quad ('X') ring in my stock slave well over a year ago now. Scotchbrite pad to clean the bore, rinse out with brake cleaner, installed, bled, riding still. Haven't bled since nor lost a drop of (the still clear) fluid in a few thousand miles. quad ring likely keeps more (all?) shit out that will abrade the bare aluminum bore and cloud the fluid (and keep the fluid in). tried to find the thread I posted in early last year but can't find it now.

 

Can anyone explain why it does this and if it is normal?

That's called "ingress dirt" Kaido. It's a natural occurrence in every hydraulic system,not just Ducati motorcycles.

As you squeeze the brake lever the pistons in your brake calipers extend outward. The sealing surface on the outside of each piston is now exposed to dirt,brake dust,moisture,etc.

As you release the brake lever the pistons now retract back into the calipers. As the pistons are retracting the wiper seals in the brake calipers are supposed to skim off all that dirt and moisture from the sealing surface on the sides of the pistons.

As good as they are though the wiper seals aren't completely 100% effective and microscopic bits of dirt and moisture are drawn back in past them every time the pistons retract back into the calipers.

Over time that dirt and moisture builds up and pollutes your brake fluid which turns it black. That's why you're supposed to periodically flush and fill both your brake and hydraulic clutch systems.