Inner Pad Wear
The hydraulic brake system on the Intruder motorcycles (front
and back on the 1400 and 1500) is a dual piston design. Unlike
the system on your car, your Intruder caliper does not slide or
move to equalize passive pressure to a fixed inside pad. Instead,
your system sends fluid pressure through the outside half of the
caliper then into the inside half, therefore applying equal
squeeze pressure to both friction pads.
Now that you understand how it works, consider the fact that the inside pad is on the end of the pressure trail, therefore any slight amount of pressure in the system will bleed off of the outboard caliper and effect the inboard caliper first. So, in effect, the inside goes to work first, followed by the outside. This is only true with slight pressure, as the working pressure is equalized when you actually use the brakes. As fluid in the system heats up, it can pressurize the pistons just enough to cause that inner pad to self destruct.
The rear system is subjected to much higher temperatures than the front. The rear master cylinder is parked next to a hot engine, it's rubber lines travel just inboard of a hot exhaust pipe, the rear caliper sits just inboard of a hot muffler (on stock LCs), and the rear rotor is not cross drilled or slot vented. This is one HOT braking system. On the other hand, the front system has no heat source other than friction at the rotor, and it is cross drilled!
So, considering the opinion that heat is your problem, and you can't fix that, you have to try to allow for heat expansion of the fluid without pressurizing the system.
1: First and foremost: Change your fluid out for Synthetic fluid (NOT SILICONE!). I personally use and recommend Valvoline SynPower synthetic Brake Fluid. Available at most any Walmart or Auto parts store for about $6.00 for a big bottle. It handles heat and moisture much better than traditional fluids, and will mix with traditional fluids, so flushing the system is easy, just keep adding SynPower until you push out all the old stuff. You can read more about it under the "Automotive Chemicals" section of http://www.valvoline.com/
2: After changing your fluid, leave a generous air pocket in the master cylinder. I personally keep my fluid level at just above the "low" mark on the window. This will make it easier for the system to release pressure as it heats up. If you want to help the system out a bit more, leave it in a vacuum state, by pumping a couple of pumps of fluid out the caliper bleeder with the reservoir closed, until the fluid bubble reaches its mark on the indicator.
3: Make sure the vent trails under the master cylinder cap are clean and not packed with dirt or bug remnants. If you look closely at the underside of the cap, it has two tiny vent trails that allow air to vent so the system can work properly. Also clean off any moisture from the top side of the rubber diaphragm and both sides of the plastic seperator. A tiny drop of moisture on that little pinhole in the plastic seperator can choke the system! When you put the cap back on, don't over tighten the screws. If you over torque the cap, it can reduce the effectiveness of the air trails.
Synthetic fluid, low fluid level, and clean upper master cylinder parts. You will still get more wear to the inside pad, but hopefully at a much lesser degree.
And if all that don't work:
The caliper pistons in this system are retracted from the rotor only by distortion of their rubber piston seals. As you apply brake pressure, the piston seals are actually distorted a bit under the pressure. Then, when you release the pressure, the seals return to their normal position, bringing the piston back with them. This movement is minimal, and is not enough to bring the piston out of contact with the rotor, but rather is intended to lighten the static pressure.
It is not uncommon for the area around the piston seal to become gummy and "clog" the movement of the seal, especially on systems that are not flushed with clean fluid at recommended intervals. If this is the case, then you will have to disassemble the calipers and clean or replace the seals. This is much more involved, so try all the other stuff first.