This occurs with our accounts as well!  Every year QB makes us RE-MAP each and every QB file.  It has to be a software bug, not a file bug.  We have 90+ different QB files and ALL of them have reset again to "Omit these payments from 1099".  I thought it was a user error last year and re-mapped without question.  But it happened again.  This is an issue with QuickBooks that needs to be resolved.  Rebuilding the data does not solve.