Weird and apparently inexplicable problem. Perhaps a commit/lock issue?
My advice is to reselect the rows in a different subjob, to force a commit after the tMsqlOutput component. Ofc you need to use a differente connection to DB for the subsequent input stage, to be sure the commit in the output stage was well done. And be careful checking the schema (number, type, order of columns: you would have one more - the auto key) in the Input stage. Something like:
[starting component of the subjob]--->row---->[...]-->row--->tMSSqlOutput
|
|
OnSubjobOk
|
|
\ /
'
tMSSInput---row--->[...]