You'll have to paste the line you are using from the nxTools config file to create the dated dir and the link to it in order for me to see what might be going on. I'm not aware of any issues with created dated dirs although I don't think I've ever done it with both the dir and link in the root dir.
Check out 'site help chattr' for how to use +l to see what symbolic links are set to point to. That should verify if /Today is a valid link or not.
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