Could the problem be explained by one of the following types of brake fade? Good luck and hope this helps.
http://www.h-e-l.co.uk/HEL_Performance_Motorcycle_Brake_Lines_Brake_Doctor_Brake_Fade.htm
There are three kinds of fade commonly encountered in fast riding; pad fade, green fade and fluid fade.
Brake Doctor - Pad Fade
Pad fade occurs for several reasons. All friction material (the materials brake pads are made of) has a coefficient of friction curve over temperature. Friction materials have an optimal working temperature where the coefficient of friction is the highest. Sometimes you can use the brakes so hard that you get the temperature over the point of maximum friction to where the coefficient of friction curve starts to decline.
The mechanics of this decline in the coefficient of friction are varied. At a certain temperature, certain elements of the pad can melt or smear causing a lubrication effect, this is the classic glazed pad. Usually the organic binder resin starts to go first, then even the metallic elements of the friction material can start to melt. At really high temperatures the friction material starts to vaporize and the pad can slide on a layer of vaporized metal and friction material which acts like a lubricant. Pad fade is felt on a bike that still has a firm, 'non spongy' feeling brake lever that won't stop even if you are squeezing as hard as you can. Usually it builds somewhat slowly giving you time to compensate for it but some friction materials have a sudden drop off of friction when the heat is put on them resulting in sudden dangerous fade.
Brake Doctor - Green Fade
This is perhaps the most dangerous type of fade. Green fade is a type of fade that manifests itself on brand new brake pads. Brake pads are usually made of different types of heat resistant materials bound together with a phenolic resin binder. These are thermosetting plastic resins with a high heat resistance. On a new brake pad, these resins will cure when used hard on their first few heat cycles. The new pad can hydroplane on this layer of excreted gas. Green fade is dangerous because many people assume that new brakes are perfect and can be used hard right off the bat. Green fade typically will occur much earlier than normal fade so it can catch a rider that is used to a certain bikes characteristics unaware. Typically the onset of green fade is rather sudden, further increasing the danger factor. Some teams have a new pads warning sticker that they place on the top yoke to inform the rider to be careful on the first few laps.
Green fade can be prevented by bedding in the pads correctly. This is a simple procedure to boil off the resins and break in the pads under controlled conditions which has been explained below - Reducing Green Fade <Top>
Brake Doctor - Fluid Fade
Fluid fade is caused by heat induced boiling of the brake fluid in the calipers. This produces bubbles in the brake system. Since bubbles are compressible, this makes for a soft spongy lever. In worse cases, the lever can come all the way back to the grip without slowing the bike.
The major cause of fluid fade is absorbed atmospheric water in the brake fluid. DOT4 Brake fluid has a tremendous affinity for absorbing water from the atmosphere, especially at high temperatures and under humid conditions. Brake fluid can absorb atmospheric water just by sitting in the brake system of your bike. A container of brake fluid sitting open can literally go bad from water absorption in an hour on a hot humid day. It is important to keep your fluid in a tightly sealed container, keeping the cap on at all times except when pouring fluid out!
Fluid fade can be avoided by running a higher grade racing type brake fluid and most importantly frequent changes of brake fluid. Regularly changing the fluid is the most important thing you can do to avoid fluid fade - change your brake fluid every 3 months and fit braided brake hoses and you will have superb brakes.
Fortunately fluid fade usually has a gradual onset, usually enabling you to either slow down or pit before a total loss of brakes occurs.
The reason we are explaining these forms of fade to you is so that you can identify what kind of fade that you are suffering from and do the proper thing to fix the type of fade that you have with the correct countermeasure. If you are experiencing pad fade, switching brands of brake fluid won't help. If you are getting fluid fade, the trickiest carbon pads won't stop you a bit sooner. If you have the finest brake parts available, you could still fall prey to green fade.