I was just about to create this issue.
It's been there for a while. I have this problem at least for 4.1+.

Here's what is happening as far as I figure out.
When you create a node with the shortcut "Control + A", the snap will stay flipped. It'll think you are still holding control.

But if you press "Control" or "Shift" once anywhere (while not dragging the node).
It'll fix itself and go back to normal behavior. That's why it feels inconsistent.
The Create Node shortcut probably forgot to update the control key status.

Here's a minimal example. Create a node with Control+A and try to move it.
At the end, I press and release the "Shift" key, and try to move it again. And it works normally.

@GustJc It's great you figured out the problem. I can confirm the minimal example reproduce the problem.
Thanks :)

The issue comes from Node3DEditor::snap_key_enabled member which is not always updated. This member variable caches the state of the CTRL key as @GustJc guessed.

When using shortcuts like CTRL+S or CTRL+A, the current implementation leave snap_key_enabled at true which makes bool is_snap_enabled() const { return snap_enabled ^ snap_key_enabled; } return a flipped value because of the XOR.