If it is working, and scanning, and then quits, I'm not sure it is anything that the software is setting. I've seen where there are frequencies the radio doesn't like and the solution for that is one of the FAQ's I sent you.
It might be something the "radio" is doing, and if that is the case maybe you should call the "Radio Shack Tech Support" number 937-395-1456 and ask them if they know why this is happening. I "do know", all radios have internal "birdies", as that is the nature of the processing when scanning. Some of those "could be" generated by certain programmed frequencies.... but that would be a daunting task to find and eliminate all of them.
If, as you suggest, the radio is stopping on birdies, then usually pressing the Lockout would enable you to bypass them. Birdies are Very Common in the aircraft bands. Mainly because if you are on CABLE TV, or your neighbors are on Cable TV, almost half the Cable TV channels are in the same frequency range as the aircraft, 118 - 138 MHZ. These signals "leak" from the cable and cause a lot of interference. Since the signals are 4-5 mhz wide AND on FM, there would not be any detectable audio.
No it has nothing to do with the trunking. This is for all the frequencies. Once I turn on the scanner after the download... it scans and stops on a few frequencies when something is being transmitted. After about 5 minutes it looks or gives the impretion that it is still scanning which it is however when someone is transmitting it doesn't stop on it. If I turn the Squelch to the side where it would make noise Static it won't anymore.
I have two scanners Pro 93 and Pro 95. The scanner I am talking to you about with these problems is the Pro 95. The reason for knowing that I'm having problems or knowing that after about 5 minutes the scanner Pro 95 isn't stopping on transmitted frequencies is because I have the other scanner going with a similar set up of frequencies and it does stop. I'm not in the situation that I don't know anything about scanners. I do know a good amount not everything but enough I have been monitoring scanners for about 4-6 years now. Please help me. It might be a situation where after uploading from the computer to scanner the birdie frequencies or Squelch on the scanner relating to the frequencies are now conflicting which is causing the scanner to stop picking up frequencies which have been transmitted on or have had activity on them.