Hi, 
I have the sames issues, stated last year, in my left leg and  ran down to the inside of my knee was sore, had to take 4 weeks of the bike. And it's never relly gone away just eases up,  it's kick of in my right leg now but I'm just manage at the moment. 
Sorry I don't have any answer just try and manage it 
Just out of interest What's your bikes set up ie pedals ect?
Cheers dave