I think this is more a hardware question that either a calibre or kindle question - but here goes.
I have my book library on a memory stick (calibre portable). Seems like when i plug in my kindle my pc fails to recognise both devices at the same time. This means I can't export from my calibre library direct to my kindle. instead i have to copy my mobi file to the hard drive, then connect the kindle and then i can copy it across.
So do you think this is a kindle, calibre or hardware problem?