Make sure you are running Trunk88 from the directory where you installed it, and that TRUNK88.CTL exists in that directory.
Once Trunk88 is running, hit ESCape to enter command mode then go to D)efaults choose I for Input (Control Channel) Parameters, and down-arrow to "CC Data Serial Port" and set that to the number (as in COMx

of the port your scanner is configured to.
Press Ctrl-F2 and see what happens.