I have never owned a D100, but I suspect it may be like the D2h and only embed a low resolution jpg in the nef file (newer Nikons like the D2x, D300, D3, etc. embed a full sized medium quality jpg in the nef).
As a former D2h user, the only practical alternative was to shoot raw+jpg which PM handles very well.
The not so practical alternatives are to sell your camera (an option I did take, but not entirely because of this problem) or to run you nef files through Capture NX which will embed a full resolution high quality jpg in the nef file (and significantly increase the file size).
Deven