@Sir Jai, in order for LNP to find DF.exe, it must be called out of a subfolder of LNP, much like the utilities. The folder Dwarf Fortress.exe file is located in, matters. It must be C:\Program Files\LazyNewbPack[0.31.25][V9.1]\Dwarf Fortress 0.31.25
With some minor alterations.. 9.3, instead of 9.1, the important thing is that the DF folder start "Dwarf Fortress", any other wording and ya get failsauce. Same with subfolders, Utilities, I imagine. Have to match up, or it won't find the folder its looking for. What kind of file structure do you have, there? If this isn't it, I dunno what to tell ya. Maybe try a clean install without mods.
What I do, is I just rename the folder. Like when I run DF_Genesis or DF_MechGenesis or DF. The one I wanna use, I rename, removing the abbrevation, \ProgFiles\LNP\DF Genesis for \ProgFiles\LNP\Dwarf Frogdress Genesis. LNP then detects the subfolder that starts with Dwarf Frogdress and hunts inside it for Dwarf Fortress.exe, let us know if you still have problems. And send us your file structure, for it. If their is no folder in LNP that starts exactly, with Dwarf Fortress, that error will show up.
Could be just a typo, somewhere, a fresh set of eyeballs might find the problem. This forum has some PC wizards in attendance, usually.