Yes, Brian had had several affairs before Siobhan appeared in the village. Their affair wasn't all that long-term. They'd only been carrying on for a few months when Siobhan told him she was pregnant. She was married to the village doctor and he was married to Jennifer. She initially allowed her husband (Tim) to believe that he was the father. They then split up and in a very satisfying scene (I'm not really violent, honest guv) he gave Brian a black eye. He then left the village, rapidly followed by the lady vicar (Janet) who had been pining for him from afar for many months.
Siobhan stayed in Ambridge, refusing to say who the daddy was. After Ruairi was born, Debbie (Jennifer's daughter from her first marriage, ergo Brian's stepdaughter) spotted that he was Brian's living image. Then the manure hit the fan big time. 
Siobhan was sure that Brian would leave Jennifer for her, but he didn't, so she flounced. However, she reaped the rewards of her scarlet woman lifestyle and eventually died of skin cancer, having pointed out to Brian (not quite in these words, but not far off) that as she had had nobody to check her back for her it was really his fault that she was dying and leaving his child motherless.
Brian was devastated and (incredibly) persuaded Jennifer to take Ruairi in and bring him up. And that's where we are now, with the ticking time bomb of Ruairi's inheritance claims waiting for a few years to pass.