AHHH-FreeScan--
Im goin out on a limb here, but heres my guess......
when you uploaded your database to the scanner via freescan, im willing to bet that your freescan is set to "Add only, do not overwrite". If it is set to this, that means every single time you upload to your scanner, it uploads your entire database without erasing any of what you had stored in the first place. So if you made several changes, then you have that channel, and every other channel you have programmed, in your scanner several times over. you need to change the setting to "Replace" or "Erase". That way, when you upload to your radio, it will either erase everything first and reload your upload once, or it will merely replace any system with the same info and add only what is different from the last time you upload.
I made this mistake as well when i first got my radio and was like--WTF?