J.,
First of all, congratulations on your new arrival! Second, don't feel bad for returning to work. Now, I'm a stay at home mom but I worked full time until my children were 4 and 2 years old. Don't beat yourself up over returning to work. You are a good mommy!
My children didn't have any eating problems when they started daycare at 11 & 13 weeks. But, since your little boy is older and has experienced some tummy troubles it could be alot different for him.
My suggestion...if you're concerned about how things are going at the daycare center drop in on them when they are least expecting you. This allows you to check on his wellbeing and get the real scoop. If you don't like what you see don't hesitate to say something immediately. If they don't take your concerns seriously then consider moving him to another facility.
Good luck and remember if you are happy your little man will be too!