You are going to obtain different tensions as the mains get shorter. As long as you're obtaining corresponding tensions on both sides, you're doing OK there. For crosses, the same applies, though friction from the mains will prevent you from truly getting the tension you set on your machine.
Just make sure that you take your time and re-review the sticky on techniques. Two other points are clamping as close to the frame as possible and if using a DW, waiting at least 10-15 seconds after the bar goes to horizontal. HTH