Hello lotso,
yes, the results of the BCO tag (or other tags) can change between simulations if the number and/or definition of tags differs between simulations, even if the definition of the tag in question (like BCO) does not change between simulations. This is discussed on pages 4 - 7 of the ISAM chemistry supplement linked from the ISAM chapter of the users guide. This ISAM behavior was also discussed in posts 11 - 13 of this earlier thread.
Christian