When you navigate "up" a directory from D:\roms, there is no way to know what paths are above it. That's why it goes to the root level. i.e
C:\
E:\
F:\
X:\
Y:\
Z:\
However, from here on out the hiearchy is built at every move. I'm not sure if this is what you mean. If you specified E:\SNES\roms\ as your roms path, and there is a folder on the E partition called "SNES" with a subfolder called "roms" and there are games in this folder with a valid extension (zip, smc, etc...), then they will show up when you pick "Select Game" in the GUI. If you navigate up from this folder, it should take you to E:\SNES\ not the root of E:\
If you are sure all these criteria have been met, can you post your path.ini?