Were the first three objects you placed the HQs? I had the same problem and it was a major pain. I had to start all over again, New, Save, Exit, restart TE, set some tiles or use your first .elv and .typ files, then set all three HQs and remember to name and zone them properly, i.e. Bish = 1st HQ =zone 1, Knight = 2nd = zone 2.
Do I have the right answer? Probably not but it worked for me.
As soon as you have the 3 HQs plus 3 fields, go in game and check it, I had problems with the fields and HQs not showing if I made any mistakes with assignments.
GL