Portable MiKTeX issues

I have installed the portable MikTeX system on a secondary drive on my dell laptop. I successfully ran pdflatex several times. I then used the MiKTeX package manager to add koma-script to the setup. Now, when I run MikTeX through the command window, the program starts up, but will not recognize a program. I even put the program to be processed on the same place (d:\miktex), but pdflatex comes back with "I can't find the file 'directory.tex'

I could install regular miktex as well, but the install issues for the regular version seem to be persisting. 

Paul A .THompson
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