I get the impression that you are not editing the batch files or creating your own. I had explained in the second paragraph of my previous reply how to create a batch file for making the help file. That gives you the help file and lets you try making a batch file.
With the newer versions of Fast lane, you do not need to use the Virtual Cables. Also, you can still use the newest versions with the scanner if you wish, it is simply a matter of setting the inputs up correctly. You don't mention having SDR dongles, if you wish to try the trunktracking, it is by far the easiest way.
In the newer versions, the format of the commands has changed. You can look at the following two batch files to see an example of the differences with the newest format
(old) FMP 20001 1 21.7 935.0
(new) FMP -i1 -o20001 -P21.7 -f935.0000
The latest version allows you to define inputs and outputs by the -i & -o rather than having them in a certain position within the file.
With a scanner, you don't use FMP but simply use the -i(input number) format in DSDPlus to get the signal to the program.
chris