I'm attempting to establish communication between my computer and a Uniden BCT15x and am of course encountering some problems. I have not found any instructions where one has to set the scanner to a particular mode in order to upload/download... Am I missing something?

Not a special mode per se, but there is a bit of setup work to be done first. You need to set up the front/rear ports as described in the FreeScan user guide...
http://wiki.radioreference.com/index.php/Freescan_-_Connecting_Scanner_to_PCYou didn't mention anything about a USB cable, but you need to load drivers, then connect the cable - that's assuming, of course, you are using a newer PC. There's a link in the article to another one that discusses that in great detail. All links are always in blue
best regards...Mike