Okay, here is whats good. I am using the English translation of TGB Dual v.7. You can find it right here.
Code:
http://www.emulator-zone.com/doc.php/gameboy/tgbdual.html
When you initialize TGB, go to File -> GB1 Load. It will load (in my case) Pokemon Red. Go to File -> GB2 Load. This will bring up another window with (in my case) Pokemon Red. I made sure that in each window I made a name and got past professor oaks intro. I saved in the bedroom and turned off both Windows. Now, I go TGB's directory and went into the SAVE Folder. Inside, I found both the save files, listed as Pokemon Red.sav and Pokemon Red.sa2 .sa2 comes from the second window, and the .sav comes from the first window. I made sure to catch a pokemon in both windows after I delivered Oaks Parcel. I went to trade in both windows and the emulator linked the windows, trading with each other. It worked just fine. My version TGB works just fine. If it doesn't work with your version, then download the one that I provided for you. If you need anymore help, I will be looking over this thread.