Lots of things can be causing this issue.

– Tightness across any combination of the quads, calves, ITB, etc.
– Mistiming of the quads
– Ankle position and arch drop
– Adductor magnus not engaging properly
– Trigger points and adhesions across various muscles leading to improper muscular balance
– Hip mobility and hip muscle activation
– Glute tightness, adhesions, and lack of activation
– Improper hip hinge

I’ve been battle this for 2 years. I’ve also been working on a lot of muscular development, which only further emphasizes properly muscle and joint maintenance.

If your knee’s are in pretty bad shape – there’s a positive side; when you use improper form, they will instantly tell you.

Make sure you’re making a solid arch and your ankle is in great position when performing a squat through full ROM.

Try out the goblet squat and find out what area’s are keeping your from dropping and ascending properly. Find the mobility exercises that address the tissue’s that are found.

Test you foot strength. See how well you can hold a solid arch.

Here’s a great video for the lower leg:
http://www.youtube.com/watch?v=ffpStkCs4ZQ