If you want, V5.3 is still available to download here
. I really don't understand what's changed in V5.4 that could affect you.
If you have time and wouldn't mind re-installing V5.4 temporarily, and seeing as you know your way round the registry editor, it would help me if you could export HKCU/Software/Enborne/Spine and HKLM/Software/Enborne/Spine, also a list of files in your install folder.
I don't know if it's a Win98 thing, but it seems odd that you are seeing some stuff plotted, but not coastline, graticule or Notams. If you don't have time, I'll still take a look around to see if I can see anything.
Thinks: I know someone else who has Win98 (or did have) and runs Spine. I'll contact him to see if he's having problems.