Motorcycle front wheel alignment?

I've been having trouble aligning my front motorcycle wheel (Honda Xr 125 L-5) I released the bottom clamp bolts and straddled the wheel until it's aligned with the mud guard and then when i tighten the forks to the manufacturers torque the wheel goes out of align again! Any ideas?

Be sure it's not the mud guard that's misaligned. Strange point of reference to use.

Put two lengths of metal or wood, straight obviously (look down the length) tight against the rear wheel, then measure the distances to the front, loosen and tighten.

Might be the fork tubes are bent, or a bent steering stem.
To check for damage -
Tighten the front axle with the wheel on as usual.
Support the bike to get the front wheel off the ground.
Loosen the fork tube pinch bolts on one side (top & bottom)
Test one fork tube at a time.

#11 are the lower pinch bolts.
http://www.partsfish.com/oemparts/a/hon/50541164f870021c54bee350/steering-stem

#12 are the upper pinch bolts.
http://www.partsfish.com/oemparts/a/hon/50541164f870021c54bee34f/handlebar

When the pinch bolts are loose, twist the fork tube around one revolution.
The fork tube should be able to spin around and around while in the clamps.
If the fork tube gets stuck at one point, there's damage.
Either bent steering stem, or bent fork tube.

Aligned to the mudguard?
WTF were you thinking?
The front wheel is the easy one unless the forks are bent.
Guessing the mudguard is out of whack.

Loosen All the pinch bolts not just the top.

Need to loosen all clamp bolts