According to all known records, John Burnett (b. Scotland 1610, d. Virginia 1686) had sons named John and Thomas. The will of John's widow, Lucretia, refers to "MY ELDEST SON JOHN BURNETT" and "my son THOMAS BURNETT JUNR." I find it surprising that the the suffix "Junior" appears on the son with a different name than his father. How unusual is that? The elder John Burnett is believed to be the son of Thomas Burnett (who died before any of John's sons were born). Would that explain John's naming his child "Thomas Burnett Junior"?
The suffix "Junior" could have been used for a number of reasons, none of which are particularly specific to the United States or Scotland. There is not and has never been a formal definition of its use. The main idea is that there was a need to differentiate between two people of the same name - usually this is because there is a father and son of the same name, but not always.
In this scenario, the most likely possibilities I can come up with are:
- John Burnett may also had a son Thomas from a prior marriage. I note that his marriage to Lucretia was somewhat late, and she was much younger than him. This may seem strange to have two sons of the same name, but it was not particularly uncommon.
- Along the same lines as the point above, John and Lucretia may have had two sons called Thomas. Whether both were alive at the same time is impossible to say. This could occur in circumstances where an elder child died, the couple wanted children named after both grandfathers (and both grandfathers happened to be called Thomas), or they particularly wanted to be sure a child would carry on a certain name. Although the emphasis is on more nineteenth century data, an interesting paper on this topic is Living same-name siblings and British historical demography by Chris Galley et al.
- There may have been an older uncle or cousin called Thomas Burnett living in the same area at the same time.
- There may have been an unrelated Thomas Burnett living in the same area at the same time (very unlikely)
- Thomas, being the second son, may have been known as "Junior", and the suffix was applied to his name for no other reason than he was familiarly known as this, or had been known as this for a long time.
If you have not already done so I would also suggest making sure you take a look at the original will. I've found a number of different transcripts online, and they vary slightly, for example one states "to my son Thos. Burnett Sern." It may just be a mistake, but if not then it could be evidence for there being two sons called Thomas.