I think in the absence of a relevant coolant temp signal, it defaults to run both fans just in case...so the ECM is probably working OK.
Check the harness grounds to the engine, I think they are at one of the tranny bellhousing bolts up top. You didn't have tranny work done or something where wiring mighta got forgotten or something, did you?
I'll think about this some more and see if I can come up with a shadetree way to verify what's happening.
When you turn the A/C on, does the compressor run? If the system is low on charge, the compressor won't run. No compressor, no aux fan, they are linked together.