Hi Trees,
I've been having a look round this morning and I don't think that the Ann Rae living with William is Isaac's sister. I think she could be Ann Griffin, who on the 1861 census is married to John Griffin and they have a son William Griffin b 1859 boarding with William Rae and his family.
RG 9; Piece: 2152; Folio: 63; Page: 30
I can't find the Griffin family on the 1881 census but I haven't had time to look any further than that yet.
I found a birth record on FreeBMD for a William Griffin in 1858 but can't see anything for a William Rae.
The county given for Maria as Ches on the 1901 census could have been a mistake on the part of the enumerator and I'm now wondering if Ann Griffin's age could also be a mistake because if this is the same person it's way out.

What do you think?