'FR' is short for 'Frame'.
I am not 100% sure how this came about, but I do know that in the old International Genealogical Index, and also the old LDS indexes to baptisms and marriages, it means that the entry is out of chronological sequence in the original register.
When the registers were microfilmed by the LDS many years ago, each page was automatically assigned a frame number. Presumably when the contents were indexed, the indexers were told to add the frame number if any entry was out of sequence.
My understanding is that when the GROS first started to computerise their indexes, they used the indexes the LDS had already created. They have since corrected and modified them, and added more information, but occasionally an old piece of information will crop up.
So the FR numbers are only useful if you are trying to find an entry using a microfilm. If you are using the online system at Scotland's People, they have no use or relevance and can safely be ignored.
As for there being two entries with different numbers, this looks as if the parish clerk has forgotten that he had already recorded this baptism and made a duplicate entry, or he has written it down again because there was something extra to be added. You'd need to look at both to see if the later one is different.
