I programmed it manually. Now I know that I have duplicate channels . Would that be a problem? Now I see that I could have downloaded software.. Which is the best software for a Whistler 1065? Should I do a factory reset to wipe off all of the other channels before I download the software?
Sounds like you have frequencies programmed in, and possibly in different scanlists, but the scanlist that contains them is not active when scanning.
The default scanlist is #1 and is active by default.
So the question is what scanlist did you put your police, fire, and ems frequencies into? Did you change them from the default of the #1 scanlist, and have that scanlist accidentally disabled?
From this distance, we don't know how far you've gone into the scanner without understanding some of the settings, and getting confused. Software won't magically fixed this.
I'd try again - reset the scanner to factory defaults because we don't know what you've done other than entering numbers.

Duplicates are not a problem, but generally unnecessary until you know that you need a duplicate. For now, you don't.
Reset, then program in your channels, but don't change the scanlist from the default. Ignore it for now. When done, hit scan. If "Nothing enabled!" shows up, hit button 1 to toggle the default scanlist on.
Have you checked in the Ontario subforum to see if your frequency references aren't stale?