Forge: 2800
Betweenlands 3.4.3
Either, it's a generation issue
See Continuity Beta 1.1.9 on curseforge.

Water generates in such a manner that if there is any block immediately above where it is supposed to generate, it won't. I happened to catch this because with dynamic surroundings flowing water makes a lot more noise than vanilla.

In this example, where the bright green blocks are, water didn't generate. Upon breaking them, the update tick caused triggers normal water mechanics and the spot fills in properly.

This also seems to happen if the area is left and rejoined, even if the offending water was fixed prior.

I couldn't reproduce this in my workspace, but I'll try with the modpack soon.

The water does generate, that's not the problem.
I believe this is actually a Dynamic Surroundings bug with Forge's classic fluids (BlockFluidClassic). As you already mentioned, after removing and replacing the swamp water block the particles and noise are gone - however after going away ~20 blocks and then returning to the block the particles and noise suddenly appear again even though the block has not changed its state at all.
Please create an issue on Dynamic Surroundings' repository and link to this issue.