Ohhh, I forget what does that, it's not really a problem, but I will ask what resolution your screen is and share a bit of info. Wait, I think it's because the tileset you have for the LNP has the graphics for the ground, which df uses period and comma and I think the apostrophe for.
If your screen is 1920x1080 then at the default zoom you should use a larger font than the 12x12 or 16x16 versions, I'm on a 21 inch monitor and anything below 24x24 just bugs me these days. It'll help a lot due to things being more crisp and making better use of the screen space available.
http://dwarffortresswiki.org/index.php/Tileset_repositoryI think there is an option to just update the LNP stuff after you drop the tileset or graphics into the right folders, but if you're already learning the game I'd check out the utilities/3rd party applications forum and check out twbt. It lets you tell the game to use one tileset for the map/graphics, and one tileset for text, plus neat stuff like being able to see multiple levels at the same time (so you could dig out a big three story cathedral type dining room and observe the whole room from the roof with the floor being visible still) and it isn't too difficult to get a hang of.
Basically all you need to graduate from using the LNP to your own mix is to keep the general folder structures in mind. Should always have a main df folder with at a minimum data, libs, and raw. You put a hack folder in there for dfhack, with the df and dfhack script or .exe (for linux or windows, I am not sure with mac), you put stuff like the phoebus or mayday graphics set in raw by just replacing the graphics folder there with it.
You add tilesets to the art folder inside of data, change init.txt accordingly.
For twbt you set init.txt so the text tileset is under graphics font, and your graphics tileset is under graphics full font.
You already made the first big step: you came here and asked a question, don't worry about the vivid nightmares pushing you towards the brink of insanity, it's normal... enough.