I had exactly this with my first. Was refered to the Fetal Medicine Unit at UCH (fortunately I was already booked in at UCH) where I had several very detailed scans. I had a whole raft of blood tests (including for cf and toxo) and a lot of discussions with the specialists. During the scans they literally counted every bone in ds's hands and feet, as the numbers of bones can be other soft markers, measured blood-flow through heart, umbilical cord and other organs - as this can also indicate soft markers, and took millions of measurements of other parts of ds. I had also had a nuchal scan and the triple test. All results were within normal limits.
The end result was that my risk of having an affected baby was substantially increased, from something like 1 in 4000 to 1 in 1500 IIRC. That may be more than twice as likely, but you've got to look at that from a different perspective as well - I still had 1499 chance likelihood of having an unaffected baby. I was offered the opportunity to have an amnio, but chose not to as the chance of having a miscarriage as a result of the amnio was vastly higher than the chance of having an affected baby.
I was scanned at about 3-weekly intervals, in order to keep an eye on ds's growth, and to keep an eye on his bowel. Although it was for a scarey reason, it was so reassuring to seem him (didn't know he was a him) and I began to enjoy all the scans!
There is another possibility, which perhaps has not been mentioned to you, and that is that you might have had a little bleed from the placenta into the amniotic sack and the baby has swallowed the blood. Because the foetus doesn't poo until birth, the stuff doesn't get excreted. This is what they said probably happened to me, as they also spotted a little bit of scarring on the placenta.
I hadn't had any bleeding during the pg. Ds was born at term, 8lb10oz, Apgar 9 then 10. So, very healthy!
The specialists and other staff were incredibly calm, patient and forthright. They took as much time as I needed, there was never any 'scaremongering' or unnecessary fuss.
I hope this reassure you a bit, and if there's anything else I can tell you, please do ask.