Can't commit both x and y, as they both refer to the same URL

I'm trying to set up a repository for my Java project which has the following
directory structure:

Project
-bin
-doc
-src

Where the "bin" subdir has the same subdir structure as "src", only the
files are the compiled versions. When creating a fresh repository and adding
everything in Project and then committing everything, I get an error like
"Can't commit both file x and file y, as they both refer to the same URL",
and it's always a file of the same name (save the extension), one from "bin"
and one from "src".

After searching the web a bit, I found that the usual cause of this is when
someone copies an SVN directory manually without using "svn copy". This
isn't the case here, as this is a fresh repository committal. I also found
that running "svn info" on the directories in question can give more info.
After trying this, it would appear that both Project/bin and Project/src DO
point to the same URL on the SVN server, Project/src. I never set it up this
way, however. Even when I make a new rep to try it all over again and add
them separately, the URLs eventually end up pointing back to the same thing
again between when I add and commit the files.

Could this be a setting in TortoiseSVN that's overriding basic SVN behavior?
How can I disable it? Also, how can I change those URLs now so that they
point to the right places, i.e., Project/bin -> Project/bin and Project/src
-> Project/src?

Thanks.

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