Check the old ECM part number, your new one is a rev C...so hardware mods were likely added, if old one was 05_ rev. Suppose the dealer might have a service bulletin why the rev change, but it would be safe to assume that was the problem.
The new ECM version (p/n 32534-05C is at least the 4th version (-05, -05A, -05B preceeded it).
CROSS REFERENCE dated January 2004:
p/n 32772-01 Use on ’01 to ’04 Big Twin EFI ECM’s (when obsolete - use 32534-05)