I suspect the errors Phoenix-D was getting and some others have had may be cause by invalid directories in that SE4Modder creates so I thought I'd provide some details on the what SE4Modder adds to the registry. (currently invalid entries are supposed to be ignored but will not be deleted)
Under the Key Name "HKEY_CURRENT_USER\Software\VB and VBA Program Settings\SE4Viewer"
there will be two sub keys "Settings" and "mods"
The 'Mods' key contains a entry with a value name of "NumMods" which is the number of mods you have opened and entries with the directory of each mod named "Mod 0", "Mod 1" etc
The settings directory will contain a vaule "RootDir" which should be the driectory of the Last mod you viewed.
I'm pretty sure I've tested the program to ignore invalid registy entries but if you find directories that don't exist here it may be the problem (and if so please let me know
)