Check your fuse for the compressor.
The solinoid that controls the vacuum that operates the flapper doors is on the same fuse as the compressor.
Also, check outside where the A/C lines enter the firewall and make sure the vacuum line is attached to the nipple that's between the A/C lines at the firewall.

1995 Trooper LS auto 3.2 DOHC /w SOHC intake
1989 Trooper 2.6 auto
1989 I-Mark RS DOHC 1.6
1991 Stylus XS DOHC 1.8