This sounds like you are just getting adjusted to the v3 scheduler and how deck limits interact with each other. But it would have been working the same way in 23.10 (when support for the v2 scheduler was dropped) as it does in 24.11 – so perhaps you are recalling behavior from an earlier version. The Anki v3 scheduler - Anki FAQs
First thing – double-check that these decks are all actually using the same preset.
Exactly how to balance the limits against each other depends on the details of your situation. Where do you want the parent deck to pull the New cards from – e.g. from any subdeck because you are gathering in ascending order, from the 1st subdeck until exhausted, in equal (or unequal) proportions from all subdecks, etc.?
Once you pin that down, you can still use a single preset to control the parent and subdecks by using deck-specific limits – Deck Options - Anki Manual – and use “Today only” on the parent deck for your New-card days.
If you explain where you want the cards from, I might have suggestions on how to set your decks, but I’ll give you an example. Let’s say that on New-card days you want 5 cards from each of your 4 subdecks, for a total of 20. You can set the Preset limit to 5, and set the parent deck’s “This deck” limit to 0. Then, on New-card day, set the parent deck’s “Today only” limit to 20 to allow those cards to come through from the subdecks.
They are separate and don’t really interact. “Today only” is the newer feature, and it’s easier to use because it makes a visible change in your Deck Options. Adjustments you make through Custom Study do not show up there.