I am posting an email I received from an Ancestry member also working with this family, and my response, to see if anyone reading this can spot any further details that I fail to pick up on which could possibly help us work this muddle out...
Fiona,
I understand your frustrations. I, too, have had problems with Isabella Armstrong. Isabella names her parents Thomas Armstrong & Mary Sinclair on her parish marriage record and on her parish death record. I cannot find a marriage for Thomas & Mary. I do find a death of a Mary Sinclair in the Pre-1855 Fife Family History Society Death Index for 5 May 1842, age 30, in Dunfermline. Isabella would have been 3 years old. I find in the 1841 & 1851 census Isabella, age 3 & 13, living with her uncle William Sinclair in Dunfermline. That possibly would make sense if her mother died in 1842. I find a marriage of Thomas Armstong in 1845 in Dunfermline to Euphemia Duff but no mention that he was a widower. This Thomas Armstrong names his parents as Thomas Armstrong & Margaret Burt. Isabella's uncle William Sinclair would probably have been Mary Sinclair's brother. I find William Sinclair's death 9 Dec 1860 in Dunfermline age 80 (so born about 1781) and he names his parents as Thomas Sinclair and Mary Mackie. I can't find that they had a daughter, Mary. I do find that they had a daughter, Margaret, born 29 1784, Dunfermline and other children, but no Mary. I thought our Mary would have been born about 1812 so that is a lot of years difference. I find Thomas Armstrong's death, widower of Euphemia Duff, 7 Dec 1897 in the Poorhouse, Dunfermline. No mention of a previous marriage.
RESPONSE:
In relation to Isabella - well, everything you write fits with what I have found so far. My only question at this stage is, how were you able to link William Sinclair as her uncle? The reason I ask this is because in the 1841/1851 census she is listed as a niece, but she could have been the grandniece of the woman living with William, Elspet Burt - sister of Margaret Burt whose son was Thomas Armstrong. The IGI has Elspet and Margaret with parents John Burt and Agnes. Or is it possible that William Sinclair is in fact Mary's father? I can't seem to find her birth details either or a marriage for William, other than him being with Elspet Burt for years.
I'm also not sure that the death of Mary Sinclair in 1842 is Isabella's mother because in 1881 she is living with Isabella and Alexander as a widow, also using the name SINCLAIR still. So either she simply had Isabella illegitimately and called herself a widow or she did marry someone else after Isabella was born are possibilities. Another idea is that the Thomas Armstrong you found who is the father of Thomas Armstrong who married Euphemia Duff is actually the father of Isabella nd not his son. It is possible that Thomas (the elder) was actually married to Margaret Burt who died and then he hooked up with Mary Sinclair - that would explain the niece connection to Elspet Burt and William Sinclair, although I don't know what their relationship is.
Unfortunately, I have no further documentation than you - no marriage for Thomas Armstrong (elder) to either Margaret Burt or Mary Sinclair. We do know that according to Isabella's marriage certificate that her father was still alive in 1855 but deceased in 1896 at her own death, although her mother Mary Armstrong (Sinclair) is not listed as deceased at this time. Just noticed that she is listed as ARMSTRONG, not SINCLAIR on the cert, will follow that up.
Or the other theory is that Isabella is the illegitimate daughter of Mary Sinclair and Thomas Armstrong who went on to Marry Euphemia Duff and had loads of children - he would have been around eighteen at the time whereas Mary would have been 25, so possible. the question then begs - why does Mary still call herself SINCLAIR in 1881 and listed as a widow and why is she listed as ARMSTRONG in 1896 on Isabella's death certificate.
Still clear as mud!
Fiona