This is because we don't have ability to reset frame size, and location correctly after loading node preset, so the workaround is to check on Shrink option for frames, and then you are good to get correct frames.

Import & Append:

Keep existing presets and if a new preset have the same name with existing preset in a folder, just keep both, rename the new preset with a name `xxx-copy`.

Import & Replace:

Keep existing presets and if a new preset have the same name with existing preset in a folder, just replace the existing one with the new one.

Clear & Import:

Just clear all existing presets, and directly import new presets with no problems.