I deal with dirty concrete all the time. I service a large grocery store chain and with the amount of traffic that goes through the back shop, the concrete gets nasty.
There are several things I would check:
1) Note if the streaks appear the moment you start scrubbing, or after a certain distance. If the problem appears after a certain distance, stop the scrubber, remove the squeegee, and look to see if there is dirt buildup between the blade and the frame. Any dust that isnt fully removed from the concrete when dust moping can build up and cause streaks on the concrete.
2) Check the evenness of the floor. If there are many high and low spots, I personally find that instead of having the squeegee at a 45 degree angle to the floor, lowering the angle to 25-30 degrees tends to cause less streaking. Make sure you don't over lower the blade, or you will leave pools of water behind.
3) Check the amount of water you are supplying to the floor. The more, the merrier. When working with VCT, a moderate amount of water tends to take off most dirt, but on a heavily soiled concrete floor, you want as much water on the floor as your autoscrubber will supply. The more dirt you emulsify, the less is being dragged on the floor and causing streaks. In fact, double scrubbing (one pass with just the pads and water, another pass with the squeegee, pads and water) is the most effective way to bring up the dirt.
Finally, be sure you are using the right equipment: pads are great on VCT floors, but they do not do a stellar job on concrete. Use brushes instead. They will get into all the little nooks and crannies and agitate the dirt that dust mopping can't remove. The key is to get all the particulate emulsified in the water so that the squeegee doesn't drag it along and cause streaks.
Hopefully this helps.