Since they don't match your menstrual cycle, it's most likely the cycle of the bacteria - and I would go so far as to guess that it's likely your immune function coming up to 'do battle' with the bacteria at that point that's causing the slight raise in body temperature.
We know that when the body's immune function 'finds' an infection, the body temp raises frequently to help attack the bacteria in the blood stream - and since this is happening every 28 days, and that's right in the right amount of time with the 'replication' of the bacteria, it's most likely your body's immune system trying to tackle the infection.
But, this is all guessing, since we can't see inside of your body to know for sure.