The ECU goes into "limp mode" whenever it reads cold temps (out side air OR your coolant). When in limp mode, you will have limited boost )7-9 psi and your timing will be retarded.
You should not be boosting until your car is up to temperature regardless.
If your temps seriously come down while highway driving, it sounds to me like your thermostat is opening prematurely.
That would be my guess.
**side note, the ECU will also retard timing&boost when it sense knock/detonation:
http://www.jekylhyderacing.com/knock.htm