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What you describe is a bug that tends to happen if you move the start date both backwards and forwards. If you go directly to the start date you want you should have colonial subjects.
If you played the game before protectorates was added England had vassals instead in India but it's wad that they are all protectorates now though
Moving backwards has not worked without issue for at-least as long as I've worked here (a bit more than 2 years) unfortunately and that's a bug that is both tricky and of very low priority due to how few actually play the later start dates. As far as I know it's not something we don't want to fix but it is of lower priority than just about any other code bug if going by the number of people impacted (I can't give numbers on how many play the non 1444.11.11 starts but as we've said before that it is very, very low).
Fixing errors in the setup of the later start dates on the other hand is something we do as they are reported. It's not the highest priority but it does get done (getting reports for such bugs however is very, very rare). I personally like the ability to pick any date a lot (even if I also end up playing the earliest possible start more or less always).
We also do frequently do update later start dates for new mechanics (you will for instance find base institution spread in later starts) or map expansions but their balancing is more or less entirely based around the 1444 start date that all but a handful people actually use
