Import from Desktop opens every folder and file on desktop?

This started yesterday after upgrading to Mavericks 10.9.5
Because my desktop is always cluttered I have a couple of folders on it where I dump everything.
As well as numerous odd items I have  folders with hundreds of photos nestling inside these 2 desktop folders.
Yesterday I had a movie file on my desktop which I wanted to import into FCP X, so I opened the Import window and selected Desktop.
Instead of seeing a couple of folders and the video, it appeared that my 2 folders had been opened and all the contents including the hundreds of photos were all being displayed.
Trashing the preferences cured it but today on launching FCP X the problem has returned.
This only seems to happen when I open the Desktop  .  .  .  it's as though the Import window doesn't see any folders, just the hundreds of files inside them, as though they were all displayed on the desktop.
Any solutions?

Thanks for the suggestion Luis, but I don't think it's that.
The folders were called Desktop 1 and Desktop 2 and had been there for months with no problems.
Suspecting that the names may be a problem I changed them yesterday to Tidy 1 and Tidy 2 but this had no effect.
Trashing the preferences seemed to cure it but when I relaunched FCP X this morning the problem had returned.
I'm wondering whether something in the latest Mavericks update is causing it.
Or is there a setting somewhere that makes the contents of all the desktop folders visible automatically?
Note that it doesn't import all the files, it just lists them in the import window making it very difficult to find a particular one.

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