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In the summer when you start the car it blows very hot air out the vents for about 30 seconds, then you hear some doors moving and you get normal air conditioning for the rest of the drive.
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That is the way the system was designed. It should blow warm the first 30 sec. to clear any humidity out of the system. This was a carry over from the previous system design.
Unfortunately, 1994 was the transitional year to the new AC controller and the luxury or checking codes and resetting codes were gone! If you have a flashing of the control display, it is trying to tell you that a code has set. The only way to retrieve the codes is with a scanner designed for that purpose. Most reputable AC shops can scan the codes and of course, as a last resort, the dealer can.
Have you checked the blend door operation, the one above the programmer? The programmer is the unit above the ECM. (The one you changed)
What model (year) “parts car” are you removing the parts from? 1994 parts, are not interchangeable with previous years!