Hi, when you set up the height and width, don't forget to set the imageheight and imagewidth also. Otherwise open NPC.txt file inside editor and you will see real-tile result of your config (edited values will be applied instantly): the collision box size isn't always equal to the GFX size, be careful!
A lot of work was done for correctly calculating any NPC's sizes by the NPC.txt's from SMBX, but for some NPC's you must define the gfx size of one frame, because it is not defined statically, always calculating dynamically or using default settings from global INI files.

Oh, and I must add a note in the Graphics glitches guide for this glitch type.
But I can improve the calculator better: could you post sprite and npc-*.txt with the defined config?
If the calculator is working normally, you can use width and height values only without creating of equal GFX width and GFX height values, but will more stable if you always define this values too. Don't forget, you always can see the result of your NPC. When creating NPC configs, you must save them with a custom sprite so you can see it's sprite render.