Running two copies of WD on one computer. Is the 2wd.txt file still the only change I need?

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It should not. . .

. . . probably because it should be 2wd.txt: Installing multiple instances of WD on your computer

You may have to start over.

If you do it properly the second instance has 2wdisplay.ini (IIRC) and wdisplayftp2 registry entries.