Evie:

Your saddle definitely needs to be raised but do it a little at time. What most fitters do is measure where the saddle is supposed to be and then over a period of time the saddle is very gradually raised to that position. Shouldn't go more than several cm at a time. That way no real shock to your body and your knees.

The most common cause of knee problems is a saddle too low but what KSH say is also true. Just get your activities whent he knee problems come up adn see if yiou can tie it to a specific event.

Good luck. Once you get that saddle raised, you will be amazed at the pwoer and strength you gain!