Strictly speaking not even a bug, merely a nuisance, but it might indicate an underlying issue in version handling.
This Version value 1.4 makes no sense in a freshly created PDF with a %PDF-1.6 header and will be ignored by a standard conform PDF processor.
So it should not be there to start with.
Its presence might indicate, though, that internally PDFBox has a non-appropriate idea which PDF version it is wanting to communicate to a processor. If so, that should also be cleared up.