With the sight glass installed inline with the valve you will have that fluctuation when using the pump. I am just doing my first real brew on the system now, but after a couple of wet runs (heheh) I decided that I really didn't like the way it works in this config so I removed it for the time being. I may install it using a weldless bulkhead, or switch to the brewhardware.com weldless flex sight glass (pretty sweet), or may even decide that I just don't need it. As far as I can tell so far, it's really only useful for measuring strike water. After that you really don't need it.
The documentation for the sight glass on brew-boss.com does address the issue of inaccurate readings & pump cavitation when the pump is going.
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As for exiting out of a brew session, you don't really. You either end/stop the session or just exit out of the program. Manual mode isn't what you'd think, Darin put up a good video (along with several other good tip vids) on youtube recently. -
https://www.youtube.com/watch?v=C-xziw2-RTk