I also have a Beta Master - When I set mine up, I turn it on last. I plug the battery in first (when stored, I unplug it), then set the screens, rough site it in (center it in line with the barrel and the target), plug in the remote readout and then turn it on. I then recheck alignment and adjust if needed for height and side to side. I handle it very carefully at this stage - making sure I do not shake it or pass any thing over one of the light sensors, like my thumb. If it gets shaken too much, the sky screens go a flying. I have shot it setting in the sun and in shade, as long as I have it centered properly, I get good readings. Even a little shift on the bags can throw it off enough to give me ERR readings - it has to be centered over the sensors when the bullet passes over them. If I get an ERR reading, after making adjustments, the next will give me a good reading. I set mine up at about the limit of the provided cord, just enough slack in it to keep from pulling the read out off the shooting table. I hope this helps. If not then you more than likely have a bad light sensor. Have you gotten good readings from it at all? - If you have, then I think it is probably set up.
Tim - I have a small ammo case that I store mine in - it is too short to glue the screens together - but I have thought of that. Once I have them set up, they are fine, but it is a pain to make sure you have tension on the screens while installing them, and not letting one slip from your grasp; or they will fly apart. I may have to get another storage container for it. The reason I plug in the battery first, is so I do not shake the chronograph and knock out one of the screens.