Anybody know if this is normal when starting to learn Sanchin stance or is there any loosening up excercises someone can recommend. its not horrible pain just a little tweaking from the tension the stance puts on my knees. any help would be appreciated.

Look at leg strengthening exercises to gradually build up muscles so you won't get any pain. Also look at the correct stance for you, it doesn't have to match your Sensei perfectly, look at the applications of the stance and if you can do this effectively.

Remember that correct human alignment and correct MA stances should be the same thing.

Strengthen your legs. But like Mal103 said you don't have to copy your sensei 100%. YOU have to find out what is most comfortable yet the most practical for your training.

I have bad knees, so my stance more relaxed, and front foot is more forward facing instead of the angle pointing in.

But to what you said when learning sanchin dachi you want to bend your knees, grip your toes, and tilt your hips up and tense. It can come across as painful until your body becomes accustomed to the foot positioning. So if you have to adjust the angle of your lead foot.

For loosening exercises use a foam roller to do a myofascial release (less tension in specific locations that your working on).

My stances are 'natural' due to my many years of training but also i understanding positioning of my feet to effectively do different techniques and moves.

I think your right on the rlaxing. i think most of my problem is i am trying to hard. from my years of shorin ryu i naturally want to move into a natural stance and am forcing my body into sanchin and putting too much strain on myself.

Sounds like you have an injury (old ?) and sanchin is finding it and triggering it off.

Most of the time, when Sanchin-dachi bothers the knees, it's because the person is allowing their knees to collapse inward. In any stance where your knees bend, your knees should track over your toes. Allowing them to collapse inward or outward from that track puts too much strain on your knees. Record video of yourself running Sanchin and see if this is what you are doing.