We have had a male guinea pig for over a year now and it is used to lying down on our lap after being patted on the back often for a while. One day there was a strip of paper on him and he ran in circles around his tray. We took it off, picked him up and patted him to calm him down but he still freaked out and run in circles and away from us.

So we put him back in his tray. The next day there was no problem. But the day after (today) he had the same problem. I touched his paw ( a usual thing) and he even licked me (also usual) then i tried to pat him starting from his nose and slowly working towards the back. He was fine till i reached the start of his crest and he freaked out. I thought it was because he didn't expect it but it always happens behind his face.
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does anybody know why he is doing this?

I wouldn't worry about it. Guinea pigs are extremely skittish, sometimes when being petted. it might be his way of telling you you're petting him too hard - especially if they make a 'rumbling' sound. I would also check to see if your guinea pig is scratching a lot or whining while you pet him because this could be a sign of mites or a skin condition. some guinea pigs also get ringworm, which can lead to dry/bald patches on their skin or ears, so I'd feel under his fur for anything unusual. I highly doubt this is the case, so only check as a precaution.

I've had guinea pigs for years, and let me tell you they all have different personalities. When they are babies, they're sometimes a bit more keen on being held and close to you, but as they get older some can be a little more rambunctious or just as calm as they always were.

I have 9 guinea pigs