I was trying to create different tabs (using YUI) to edit a form. I wanted to create a separate tab for each of the field groups. However, in the form_alter method of the form for my module, I could not see the fields in the fieldgroup. On debugging I found my fields in the fieldgroup to be present in the form_alter of other modules. Problem: The CCK fieldgroup module has a weight of 9. If your module has a weight less than 9, then it is called before CCK fieldgroup, hence the problem. Solution: Set your module's weight more than 9. The setting is in the system table, under the column weight. This fixed the problem for me. It took a long time to solve the problem and thanks to some of the other posts mentioned below for writing about this.
1. Benjamin
2. Andy