Coming from Survey controller and survey pro. I remember when. Setting up on a known point you would just measure from the point to the cross hair on the S7.
Now using SCS900, when setting up on a knowm point the HI seems like it doesn't like when you use the vertical measurement at an angle. So you really have to level over and measure up? I have done the setup three times and was always off 0.06' which on the other software it would take it just fine measure at an angle.
With an instrument height of 2.00' you might see an error of just over 0.02'. At an instrument height of five feet your slant measurement would be slightly less than 0.01' longer than a true vertical measurement. Your 0.06' of error is coming from something else. Perhaps the software allows you to designate what you are measuring to like the bottom notch or a true vertical measurement. I would look there for a resolution.
Check the settings for the prism, check for quick release option, also check the pole point. I've seen pole heights off like that from worn points.