By chance, did you create two entirely different files in PSREdit500? One file with trunked systems. the other with conventional frequencies"?
For the WS1040, and the related models using the same Object Oriented programming (such as the WS1065, original PSR-500 & -600, among others), you can only use one file at a time. While you can have additional programming files stored in the various V-Folders, you can only scan one at a time. So, if you have a file with only trunked systems, if you were to upload a second file with your conventional channels, then that would override your trunked system programming, and the only thing you'd hear would be conventional systems.
You need to program your file with whatever trunked and conventional channels you want, all in one single file. You can still control which ones you are hearing by using separate scan lists, which you can toggle on or off whenever you wish.
As bob550 has already noted, you can import the conventional channels you want into your existing trunking systems file, then load the expanded file, containing both types of systems, to the scanner.