The clutch does two things;
1.. When coming off a corner, it holds the engine at a given RPM. That RPM depends on the settings of the clutch. The torque it's holding is transferred through the chain to the rear axle.
2. It makes heat. Heat is a power loss, less power going to the rear wheels.
If you set the clutch to stall at the engines speak torque RPM, you're getting maximum torque to the rear wheels. Above or below that setting, less torque is getting to the rear axle. Less RPM less torque to the rear axle means less horsepower at the axle. RPM x Torque / 5252.1 = HP.
Unless there's something wrong with your clutch, like a bearing going bad, a sprocket wearing out, a drum rubbing against something, this is how it works. As long as the clutch is letting the engine rev to peak torque RPM, it's got to work. Once the engine RPM, divided by the gear ratio, is the same as the axle, then the horse power is the same at the engine and the axle.