First, that model scanner is too "senior" to deal with Phase II systems. You'd need the newer model BCD325.
Did you use a program such as Freescan, ARCXT or ProScan to download the desired system? Going this route will ensure all the correct parameters are set when the data is imported. If you do it by hand, errors (such as system type) have been known to happen.
And assuming you are like all of us once were, a "newbie", let me ask if you downloaded both site(s) data as well as talkgroup data? Sometimes new folks (and us veterans) sometimes omit one or the other.
The last thing I suggest when someone is at wits end on trunked systems is this: Download all of the site frequencies (frequencies only, no talkgroups) as a conventional (not trunked) system. It has to be manually done unfortunately. Then scan this as a regular system. The scanner should stop on a frequency that has a "motorboat" like sound, which is the control channel. Tap the Lockout (L/O) button, then continue to monitor. If you hear voice, that confirms you are within range and the scanner is capable of "hearing" the system. If nothing else that is a good diagnostic test and you have the frequencies stored if the system goes into the very rare "failsoft" mode (where trunking controllers fail).
Following that, re-program as a trunked system.