For all my ba flights that i've checked my e-ticket receipt for via Amadeus japan
https://web.1a-xml.jp/eITR/WebEITR/WebEntry.aspx it turns out that there are 2 PNRs. The normal ba confirmation ref is shown as being the 1A amadeus PNR while another PNR usually beginning with the letter "R" and has, like the 1A one, 6 characters is shown as my BA ref, although I can't access it via mmb. I believe I have also seen this type of ref printed on my baggage tags, and I always wondered what it was for. Does anyone know? Try checking your e-tickets via that link and see it for yourself. It could be for another GDS.