The iPod could definitely cause a problem as Calibre only shows the first supported device that it sees. However you should have been seeing Calibre displaying the fact that it thought an iDevice was connected in the message at the bottom of the Calibre window.
The best thing to do is probably to disable the Apple Device driver under Preferences->Plugins. This will stop the iPod from being seen directly by Calibre so that the Kindle is seen if both are plugged in at the same time. If you want to send books to the iPod you can still o so using the Calibre Connect to iTunes feature.