Are you going step by step by the manual? I don't have the scanner, but I am going by the online manual
http://www.uniden.com/pdf/BCT8om.pdf
How are you trying to program the system? Are you using Control Channel only or putting in all the frequencies? I assume you are using information from the database?
http://www.radioreference.com/modules.php?name=RR&sid=844
If you are putting in all of the frequencies did you:
Press trunk for 1.5 seconds
After two beeps select the bank you want to put the system in
Select E2-800 using the up and down arrows press E
Select Prog F and press E
Enter the frequency and press E Make sure there is a M to show Motorolla
Press arrow key to select next channel and press E
repeat until all the frequencies are entered
press SRCH
I hope this helps