Got it, let's figure this out. Can you explain to me the part that doesn't seem to "take". Paint the picture for me of your process.
1. Does the "Send to Scanner" upload process of Freescan to the radio complete without any error?
2. When you Send To Scanner, are all the Systems selected, and the options listed on the right such as "Send Custom Radio Settings" etc. are all checked?
If the upload Send To Scanner process is clean, then it's probably what's called the System Quick Keys, where in FreeScan, your System Quick Keys default to . or 1, but they might not be active by default in the scanner. I got bit by this when I first started with FreeScan. Can you send me a copy of your FreeScan program file, the .996 file? Email me with my nickname above at gmail. That will let me see what you're dealing with and help direct what to press on the scanner to get it all working.