I noticed this too with any sideloaded books, whenever you open another book or Newspaper.
I agree, very frustrating...
B&N has known about this bug for a long time. Apparently fixing it isn't high on their priority list. See, for example:
There were also, if I remember correctly, discussions about it on the Issues Reporting boards, which were hidden or deleted several months ago (the boards, that is, not those specific discussions). Until the powers that be decide to restore or revive those Issues boards, it's hard (all right, impossible) for us ordinary customers to know which issues have been reported and which, if any, are being worked on.
Thanks for the links! It doesn´t happen with all books, my side loaded are generic formatted ePubs.I opened another book, read it halfway, put a note and it´s still there. I´ll try reformatting it specifically for Nook ST and see if it works.