Hi, Jan.
With ver. 6.0 (and prior), the phase number acts mainly as a label, and doesn't itself dictate the phase sequence (i.e., the order, or the simultaneity, in which movements are served). Instead, the phase sequence is determined entirely by setting the protected-turning phase sequence to either None, Lead, or Lag.
You can set the phase numbers, independently, by clicking on the movement arrow button, setting the phase number, then before clicking OK, making sure the boxes in the right panel read "Apply all items to this movement on this approach of this intersection".
Let me know if this doesn't resolve the problems.
Please note that the final release in the ver. 6.0 series was 6.0.0.46. You may download it freely. You won't have to reenter your license information. It fixes a few bugs in the version you're using. To download it, click on the Download link (
http://www.tsppd.com/downloads.htm), then and click the Archives link at the bottom of that page.
Regards.
Greg