I have a Brenspeed tuned SCT that I have running my my stock engine 05 5sp 4.6. Now that the weather is getting hotter, I have had to use the A/C a couple times. The first time I turned it on, it wouldn't blow cold air, so I pushed the A/C button on and off repeatedly (the light turns off and on). Normally you would hear the compressor click on, but not this time.
After about a minute or so, it decided to blow cold air.

The next time I tried the A/C, the same thing happened. The car has about 65k kms on it and I have never touched the A/C system. The air blows very cold once the A/C comes on.

Could the aftermarket tune be causing this? Believe it or not, I just have not had time to download the stock tune to see if it makes a difference. I only have time sitting at my computer at work on my break to type this.

 

So you never had any AC service, because early 2005 and 2006 had AC clutch failures. There is a revised design A/C compressor clutch that has been available.
Maybe yours took this long to start going bad.

 

Never even heard of this, surprised. Of course, now out of warranty I am out of luck. I will download the stock tune and see if it makes a difference.

 

I've noticed that if I disconnect the battery for any reason, when I go to use the AC for the first time, I need to cycle the "temperature" dial all the way from cold to hot, then back to cold, before it will blow cold air. I think it needs to learn the range of the dial.

You might give that a shot, it's an easy check.