Hoggle,
I have had problem knees over the last 15 months.
Not too sure what you are suffering from but I find squats and building strength in your quads is quite beneficial.
There was a whole section dedicated to knees in one of the recent issues of RW - think it may hve been May or June. This gave information and advice on how to keep your knees healthy.
Do the muscles in your legs feel tight? You may need to do some stretching exercises. Do you have an osteopath?