I have developed a bit of a knee problem (I think I have a Patellofemoral Syndrome) as a result of a tendency to move my knee towards the top tube during the down stroke.

So my question is, how to solve this problem?

Thanks, Blaz

Is there a chance you could see a doctor to confirm what you have?

The reason being is that there are so many different explanations as to why you are having knee pain. I've heard of at least 2 other knee problems with very similar explanations of the symptoms. I see you live in Slovenia, so I am unsure what you guys would do to get to a physical therapist. It may be a good idea to make sure this is what you have before you begin looking for a solution.

Having said that, it looks as though the article explains how you can solve this problem- doing leg strengthening activities (weight training), ice the knee when feeling pain (I would also alternate that with a heat pack and keeping the knee elevated), taking anti-inflammatory agents (aspirin), and working on developing your pedal stroke. When you do your weight training, start with light weights and lots of repetitions. As your muscles become strengthened, you can add more weight, and eventually, you will have strengthened the muscles around the knees to the point where the knee pain will be alleviated.

I know this is going to sound insane, but as you work on your pedal stroke, consider taking kickboxing lessons- why? Because those front kicks in kickboxing develop your hip flexors, which are traditionally very weak muscles, but do aid in a stronger, more solid downstroke.

Firs and foremost, see a doctor if you can to confirm this is what you are experiencing. Then see if you can get to a physical therapist once or twice- just so they can help take you through some exercises in a safe and effective manner. If you can't get to a physical therapist, then a personal trainer who has knowledge of physical therapy techniques.

Koffee

Make sure that your pedal axles are not bent, this can play hell with problem knees. Are you using a clipless system? Are the cleats correctly setup? are you using cleat with some rotational float ?
As a less stressful alternative to kickboxing, try Tai Chi Chuan, it will excercise the same muscle groups and joints without the impact.