Hi Shessi. 99.9% of all 3rd party aircraft for FS98/CFS1 (& many early FS2000/CFS2 models) were created either with the original BAO Flight Shop/Aircraft Factory or Aircraft Factory 99 (AF99) the updated version. There's no reason they will not work in CFS2 & this is not your problem. I suspect you're using WinXP. Some 3rd party aircraft that work perfectly well with Win98/Me conflict with XP. Some early CFS2 models also have this bug. You can fix it by patching the MDL file with the MDL Repair Utility. Check out my CFS2 FAQ page for a link.
http://www.simviation.com/lair/cfs2faq.htmIn the model folder is an .mpi and a .nmp?
These are backup files for Aircraft Animator. You can leave them where they are or safely delete them.
It's entirely your choice but the later FSDS2 & Gmax CFS2 aircraft are far superior to the older CFS1 models in every way.