First of all, the difference in capacity is actually greater than you included. Dragon launches without a fairing, thus there is an increased capacity as a result of launching without the fairing. The exact mass isn't known.
Okay, so what else might be different in the cargo capacity? Here's a few things:
- The Dragon might not be structurally capable of carrying more than that weight given the vibration requirements imposed on launch.
- Fuel mass (Unlikely, however, to be 2.5 tons)
- The ISS orbit requires more fuel to achieve than the referenced LEO orbit. This is quite likely to be a major contributor, accounting for over a ton reduction in mass to LEO per the old Falcon 9 user's guide.
Bottom line, I think the loss in mass is partially due to the inclination, partially fuel, possible some other consumables (Port covers, etc), and the remaining portion being deliberately keeping the capacity lower to ensure there is sufficient margin in case of sub-optimal performance.