When I set up my draft order one of the teams (my team) is skipped until the next round. This is a keeper league with two keepers. I do not get a pick in the 3rd round.

Hello -- can you tell me which tool you're using to set the draft order?

In the draft dominator I went to setup and set draft order. Also under Team Stats window it shows this teams next pick in the 4th round and all others 3rd round.

Ah, OK -- let me move this over to the Applications forum.

Open your league file (*.ddf) with notepad, and delete all the lines under the Team Section, Draft Section and Keeper Section. Save it, and then open it in DD. Sounds like you started with last years league file, and have a ghost. In the future, always save your league before you draft or add any keepers. Then after the draft, save your league with another name. That way you will always have a blank league with your league variables to start with each year.