Hi Andrea, 
I could see large alignment errors with pole master if I didn’t have the gain / exposure adjusted to see the required dim stars in the monitor step.  I use the second step for both Gain and exposure.  So even though you can easily see Polaris with the lowest Exposure/gain, you should turn it up to see some of the dimmer stars around Polaris.   One way to see if gain is too low is to look at how stable the image is in the monitor step.  The two white boxes On the big screen should be stable and tracking 2 stars.    This should allow you a good polar align with the red/green pole boxes in the small monitor screen.   My guess is you’re only getting a good initial align to 5 arc minutes which is what I was getting until figuring out the monitor step wasn’t stable.

this was my problem, and once fixed my alignment results in little dec guiding input with the Mach 2.   

other than this, make sure the camera is mounted solidly and not able to move, and if you do remove it or adjust it at all, you need to recalibrate it’s centering in the app.     

terri