Well I've spent over an hour trying to create a merged patch using various versions of FO3Edit, and I give up for now. The current version doesn't allow me to right click in the left panel at all, and the older versions don't give me the option to create a merged patch. Any advice would be hugely appreciated - I'm sure I've done this successfully in the past...
EDIT: As a side note, DaRN UI is pretty much unusable. All of the font is too large and overlaps into an illegible mess - I've no idea if this is to do with FWE or not but I figure it's worth a punt.
I'm afraid both the above problems have something to do with your specific installation, my friend - I've had no problems whatosever creating a merged patch with FO3Edit, and Darn UI has been tested several times and works fine with FWE for a lot of ppl.
Perhaps you can post your load order to have us take a look, although the problems you mention seem most likely to come from a corrupted installation, and may require a complete reinstall...
EDIT: Actually, let me take a stab at a few more obvious solutions to your problems:
FO3Edit issue : firstly, always use the most current version - there is nothing to gain by going to previous ones... the fact that it will not let you right click in the left panel means that it has not finished loading the resources - you are either trying too early without letting it finish loading, or it gets stuck in which case there should be an error message in the right-hand side mentioning the type of error and the problematic mod
Darn UI issue: did you install the FOMOD via Fallout Mod Manager? If not, did you edit the fallout.ini file to use the right fonts as per the read me? Your problem seems to me to come from using the default fonts instead of the Darn UI ones
Best of luck, BDW