I had another look at your logs, in the first case the subtitles were part of the TS stream stored as closed captions. You were using a custom profile which instructed handbrake to use those built in closed captions and preserve them, which is why it worked:
2019-09-27T08:19:21 MCEBuddy.AppWrapper.Handbrake → + subtitle tracks:
2019-09-27T08:19:21 MCEBuddy.AppWrapper.Handbrake → + 1, español, Closed Caption [CC608]
One thing you can try is, enable the Skip remuxing option in the expert settings which will allow handbrake to work directly on the original M4V file instead of the remuxed TS file in the second case, it may detect the built in subtitles and work with it.