Oh no, what a pain (literally). Is the pain back in the area that had the MFX or does it feel like a general kind of "overdone it" type of pain? Any swelling? Does it respond to ice? I guess that hopefully you've just done a bit too much and the MFX site is feeling a bit niggly and has told you to back off. I guess it *could* be any number of things - worse case the MFX might be seriously unhappy, but it could well be that the knee is just feeling a bit overused. I know somewhere else you mentioned some patella damage - well, it might be nothing to do with the MFX but the increased bits of running/biking might have started that to feel a bit inflamed. I get miles more symptoms from my patella wear than from the OCD lesion - in fact the only reason the OCD lesion was found was due to the MRI for patella problems and I'd say that 5% of the time the lesion bugs me (wrong angle with weight) but 95% of my problems are patella based - typical PFS symptoms of aching, burning after too much exercise, strong dislike of hills and stairs, sitting with knee bent for too long, squats, lunges, extension with weight etc, loads and loads of grinding - always patella never femoral condyle area.
Not sure that tells you what to do next - I guess given your history of MFX I'd be seeing if a couple of days of complete rest and ice and all the usuals helps things - perhaps try and whack in some stronger NSAIDs in case it is patella irritation (sometimes a day of Naproxen kicks mine back to tolerable level) but if things get worse or don't improve then a visit to the OS might be required.
Really hope things settle down, all fingers crossed.