Well, it could be a number of things actually. A quick check of the web comes up with the following (bear in mind it was written by a British guy so some of the spelling may seem odd and the medication he refers to is your average over the counter anti-diarrheal, half of a tablet crushed up and fed to the pet)
Read on to see what they said, (Good Luck)
Diarrhoea can be as minor or as major a problem as it can be in human beings
The number one rule is that if the diarrhoea is fluid and has the added symptoms of the guinea pig's coat being fluffed up and it is sitting in a corner looking thoroughly miserable then it is a major problem. It must be taken to a vet P.D.Q., for it will be in need of an antibiotic, and quickly!. There are several diseases that guinea pigs can suffer from which can prove rapidly fatal and the symptoms I have just described are indicative of them.
If the diarrhoea is fluid but the guinea pig is alert and though not eating as well, at least interested, the first thing to do is give it half a tablet of Diocalm, powdered down and given mixed with a small amount of water. This is a product formulated for human beings who have diarrhoea which is very safe and effective for use upon guinea pigs. The next thing to give, and this is very important, is a tablet of Buscopan, powdered down in the same way as the Diocalm. This is also a human medicine, which is a gut relaxant and analgesic. This eases the griping pains as it relaxes the gut spasms, which makes the animal feel better, which is half the battle.
Repeat the Diocalm every ten to twelve hours but as soon as there is a sign of things beginning to firm up, stop the treatment. Usually two to three half tablets are sufficient.
If there is a general softness of the pellets then just one half tablet of Dioclam will usually clear things up and the Buscopan will not be necessary.
In cases where this kind of diarrhoea lingers or is spasmodic, the powered astringent and delmucent herbs such as Slippery elm, Carob, and Shepherds purse can be used more long term. If the latter is available to be picked fresh then feed it to the guinea pig direct.
In all serious cases of diarrhoea it is essential to keep up the body salts with rehydration preparations. A quick comparison between those formulated for human beings and those licensed for animals quickly shows that they are almost identical, for we are, after all, both mammals!. The big difference of course is in the price, the veterinary products, as usual being far more expensive. There are several on the market, Rehydrate and Dioralyte being just two. Give little and often.
There can often be a flushing out of the gut flora which is vital for the guinea pig to be able to digest it's food so it is always wise to give some form of probiotic to help reseed the gut. Avipro is the one I use, available from most large pet shops. Just a pinch in a small syringe of water once a day for two to three days.
DON'T TAKE CHANCES WITH DIARRHOEA. IF YOU CAN'T NIP IT IN THE BUD WITHIN THE FIRST TWENTY FOUR HOURS OR THE GUINEA PIG APPEARS TO GET LISTLESS IT NEEDS DEEPER INVESTIGATION.