Hi Ted
Dunno where the PM is hiding then. You should see a notification for it. We'll have to get Andrew to go in with the toolkit and look for a fix. I looked but everything seems to be ticked off just as it should be. Anyhow.....
I've got good news!!

To answer your question...yes it appears that the first Susan probably died and they had another. Not unusual at all. It's also possible that the first Susan did not die and they used the name again for some unknown reason

. Actually I don't know of a case when this happens with a female name but there are surely documented cases of more than one male in a household with the same given name......(I think it's just to confuse us researchers!)
Now for the good news.....
When you run a parent search on the IGI you only get 3...
JEAN PAGAN THOMSON - International Genealogical Index
Gender: Female Christening: 14 FEB 1836 Troqueer, Kirkcudbright, Scotland
SUSAN THOMSON - International Genealogical Index
Gender: Female Christening: 04 APR 1828 New Abbey, Kirkcudbright, Scotland
SUSAN THOMSON - International Genealogical Index
Gender: Female Christening: 03 OCT 1841 Troqueer, Kirkcudbright, Scotland
But when you look on the BIVRI disk set (which I just so happen to possess

) you get this:
THOMSON, Susan Christening
Gender: Female
Birth Date: 31 Mar 1828
Christening Date: 4 Apr 1828 Recorded in: New Abbey, Kirkcudbright, Scotland
Father: Alexander THOMSON
Mother: Elizabeth SMITH
Source: FHL Film 1068034 Dates: 1820 - 1854
THOMSON, William Glassel Christening
Gender: Male
Birth Date: 1 Sep 1830
Christening Date: 7 Sep 1830 Recorded in: New Abbey, Kirkcudbright, Scotland
Father: Alexander THOMSON
Mother: Elizabeth SMITH
Source: FHL Film 1068034 Dates: 1820 - 1854
THOMSON, Robert Christening
Gender: Male
Birth Date: 12 Jul 1833
Christening Date: 29 Jul 1833 Recorded in: Kirkbean, Kirkcudbright, Scotland
Father: Alexander THOMSON
Mother: Elisabeth SMITH
Source: FHL Film 1068032 Dates: 1737 - 1854
THOMSON, Jean Pagan Christening
Gender: Female
Birth Date: 2 Feb 1836
Christening Date: 14 Feb 1836 Recorded in: Troqueer, Kirkcudbright, Scotland
Father: Alexander THOMSON
Mother: Elizabeth SMITH
Source: FHL Film 1068035 Dates: 1764 - 1855
THOMSON, James Christening
Gender: Male
Birth Date: 8 Aug 1838
Christening Date: 19 Aug 1838 Recorded in: Troqueer, Kirkcudbright, Scotland
Father: Alexander THOMSON
Mother: Elizabeth SMITH
Source: FHL Film 1068035 Dates: 1764 - 1855
THOMSON, Susan Christening
Gender: Female
Christening Date: 3 Oct 1841 Recorded in: Troqueer, Kirkcudbright, Scotland
Father: Alexander THOMSON
Mother: Elizabeth SMITH
Source: FHL Film 1068035 Dates: 1764 - 1855
Looks like your William had an interesting middle name!! ALso looks like he took a few years off his age in later years as I had him pegged for 1834!! And you get the bonus of actual birthdates in addition to christening dates on some of them. You might want to take a look at the 1841 census and see how many of them were still at home and the ages just to see if this all lines up for you.
Hope that helps you!
Best wishes
Jean