Hi sunshinebaby,
Just to clarify, by "I didn't download the 1st semester" do you mean you already have the Semester 1 lessons in your second computer? If you don't have it, then kindly import Sem 1 as well.
Does the "missing files/media" problem happen only in Semester 2, or does it happen in Semester 1 as well? Also, are you missing the media files for all your lessons, or only for specific words (or categories)? You can counter-check in your "My Documents \ BrillKids \ Little Reader \ Media Library" folder if you have the "missing" files to see if they're already in your computer but they are just not playing in Little Reader.
Let me know if you are missing all your media files (or just the files that are missing) so I can send the files to you
As for choosing "Run" instead of "Save" when downloading, this shouldn't cause the problem you are experiencing, although it would be better to actually save the file to your computer in case you'll need to use it again later on (this way you don't have to keep re-downloading these files, except when you need to upgrade to the latest software versions).
When saving the file, some browsers will save it to your "My Documents \ Downloads" folder by default -- after completing the download you can just get the file from there and transfer it to a place in your computer where you want to keep it. Other browsers will prompt you about where to save the file -- you can then select your preferred location (say, just in your Desktop) and your file will be directly downloaded and saved there.
If you noticed, you have an "Import-Export" folder inside your "My Documents \ BrillKids \ Little Reader" folder (this is automatically created when you installed LR). You may choose to always save your downloaded LR files from the Forum Downloads Library, so you can always find the files in one place when you need them.