Hey nohmi2,
Do you mean that your Story doesn't come up with the screen that allows you to choose between charging the battery and connecting to your PC? Mine does that too, on occasion, and from what I've read, many ereaders that connect via USB do - it's not just iRiver that has this problem.
I usually find unplugging the USB cable from the base of the Story, then plugging it in again, seems to work. And I've found it works most reliably if I make sure the Story is switched on before plugging the USB cable in - then you have to be quick and jump on the menu option to connect, before it times out. But it is a bit bewildering, isn't it, that it doesn't seem to work predictably?
In response to some of your other questions or comments so far: are the ebooks you're trying to manage ones you've bought from online stores, or ones you've found by other means? It does make a bit of a difference. If you're converting other documents to epub format, then Calibre is a useful option, though I personally don't care for the file management side of it (just personal taste, not criticism of the program). If you;re just wanting to convert files to epub format so they display well on the Story, you might want to look at
http://ebook.online-convert.com/, which does the conversion (I think it uses Calibre anyway) without your having to generate database entries for the file, or else
http://code.google.com/p/sigil/wiki/ConversionChart, which provides options and tools for a range of file types. The epub editor Sigil that the second link points to is a very handy app to have if you want to modify epubs, and it's free, but it's a bit effort-intensive, and isn't nearly as automated as people are used to with apps like Microsoft Word.
Good luck with it all, nohmi2!