I had an amniocentesis which was normal, but the baby appears to have a cleft palate on ultrasound. Why wasn't this detected on the amnio?

This is common. Amniocentesis will not show most cleft fetuses because we don't know the gene problem most of the time. In fact, even very sopisticated gene testing will show the genetic causes of cleft lip and palate less than 20% of the time. This field is still very young!
Not chromosomal. An amniocentesis detects a very specific kind of problem. It checks for the number of chromosomes the baby has. Normally we have 46 chromosomes that carry our genes. Some babies may have too few or too many whole chromosomes. A cleft palate is not necessarily caused by a problem in the chromosomes. Sometimes external factors affect the way the palate is built even with normal genes.
May be isolated. A newer genetic technique that looks for errors in smaller amounts of genetic material ( microarray, cgh, ) is not standard on amnio's yet, but can be done on baby. If it is an isolated congenital malformation, that may be normal, also. It's good news that your baby doesn't have a chromosomal abnormality.