Er, not exactly mono; rather single channel mono unless you make up your own cable. This involves a single circuit (mono) plug on the scanner end and a two circuit (stereo) plug on the sound card end with both "hots" connected together feeding both inputs equally. This may be part of that sound card "issue", then maybe not in a world of many variables but use this cable and that aspect is eliminated.
The most common problems are incorrect sound card "mixer" settings. It's not a one size fits all world with so many sound cards and software programs for them, Windows Mixer Panel default won't handle the complexities of those fancy Surround Sound multi channel options. Linking itself to other software it SHOULD make them run in tandem but this can lead to problems (the rule of unintended consequences) so it's a good idea to look into everything and make sure the settings are right for the device in use at the time.
Then there is interaction with the recorder software as well, there are times when I wish I could find the suspect .dll files and blow them away. Since we're not all electrical engineers and computer geeks around here all I can say is thoroughly investigate, learn as much as you can about how these programs work and above all GOOD LUCK. If you find yourself pulling your hair out just shave your head; it's the "in" fashion and it's summer, nobody will notice. (;->)
Percussive maintainence;
If at first you don't succeed try a bigger hammer. If all else fails explosives are the solution.
