So you are saying you have the exact same file locations on the external and one system reads it, while the other does not?
The extension refers to the letters or numbers after a file name so file.exe is an executable file while file.bmp is a bitmap files. If it is an extension issue, maybe you have some files with strange extensions.
Some virus scanners throw a fit if a file has a double extension like file.bmp.exe . This is because MANY viruses try to hit computers that way.
In fact in the WORST idea ever, Microsoft make hide known file extensions ON by default making this problem quite bad as unknowing users could download a image file(the file above would look like file.bmp only and not file.bmp.exe) that was actually an executable(that could do just about anything.).