Certainly looks like you may have found the reason why

No more clues regarding parents from the names of John and Jane's children:
1. GEORGE THOMPSON Birth: 24 JUN 1855 Melrose
2. WILLIAM FULTON THOMSON Birth: 15 AUG 1857 Ladhope
3. JAMES THOMSON Birth: 26 MAY 1860 Ladhope
4. JANE RENTON THOMSON Birth: 25 OCT 1862 Ladhope
5. JOHN THOMSON Birth: 14 AUG 1865 Ladhope
6. HENRY THOMSON Birth: 05 AUG 1868 Ladhope
7. JANET THOMSON Birth: 14 JAN 1873 Ladhope
Steve, may be hard for you to properly verify mother's details. Hector Hall looks to have died in Castleton in 1875 going by general searches on SP.
The only document I can think think of at this stage that might provide more information is perhaps John's death entry, which might include a possible married name for Janet his mother.
Monica