I definitely agree that you may want to call the mom and ask her if she would like to come over one day and watch the 2 kids playing, maybe that will instill a sense of security. If she does not understand how children think and how they react then she may not come back. Let her know that it takes at least a couple of weeks for the children to get to know each other and feel comfortable together. It is hard for your own children to share their home with strangers, he may feel threatened by the attention you give to the daycare children. I had the same problem with my 2 boys (expecially the younger one), until we bought a home where the daycare children are downstairs and do not enter my boys bedrooms or living area. This seemed to help a lot.
If this mom does not come around you may be better without her and put the word out for someone else. It is a tough time, but we have all gone through issues such as these with parents. Sounds like a first time mom to me. Good Luck