Company A starts Company B with the intention of Company B being a client for Company A. Company B is a non-profit and it has a separate board (no one on from Company A is on the board for Company B). Company A is loaning Company B money to start up.
Some questions:
Should Company A's CEO be managing (micro-managing) Company B employees?
If they are, can you lose the non-profit status?
Are there more serious ramifications that the companies can face if determined to be a essentially the same company?