I added tags to this post to increase visibility.
Would you mind re-checking the version of ChemStation that you are using by going to Help>About? There was never a B.03.03 version released for the legacy GC/LC ChemStation.
Are any changes being made to the method before starting the sequence or while the sequence is running? There are a few entries in the Known Problem Report related to GC's regarding the "modified after loading" flag, but nothing for HPLC instruments that I can see: https://www.agilent.com/cs/library/support/patches/ssbs/G2070BA.html