Version:           0.9.6 (using KDE 4.5.90) 
OS:                Linux

Example:
On my system the default Okular handler for PDFs is the command
okular %U %i -caption "%c"
This is the vanilla setting, I can’t remember ever having changed that. Plus, this system was freshly installed less than two months ago.

Klipper does not handle this properly, as it opens two Okular windows. Example: I Ctrl+C a PDF file in Krusader/Dolphin, the clipboarded string is file:///path/to/some.pdf. The menu pops up and I select Okular. Now I get two empty Okular windows, with the Window titles %c and %c (2) respectively.
One says "/home/frank/Dokumente/%i could not be opened.", the other says "/path/to/some.pdf could not be opened." /home/frank/Dokumente/ is set as my documents folder in my personal settings.

If I open /usr/share/texmf-dist/doc/latex/pdfpages/pdfpages.pdf (copied from a locate search result in a terminal), I get two windows as well, but only one is empty, the other one shows the file, with the window title "The pdfpages Package - %c". For comparison: opening the file normally via $filemanager, the window title reads "The pdfpages Package - Okular".

So the file:// URI is another problem here.

Reproducible: Always

Steps to Reproduce:
Copy a file or URL to the clipboard and, from the Klipper popup, select an action that is associated with the file type.

Actual Results:  
Multiple windows open, of which only one opens the file, the other one gives error messages due to additional parameters in the selected open command.

Expected Results:  
Only one window should open and then process the selected file, the parameters should be either correctly dispatched or ignored if the former is not possible.

I’ve been observing this problem for a long time now, it must go back to at least 4.4, quite possibly even farther.

PS.: My Klipper version is 0.97, KDE is at version 4.6 RC2 (both are not listed in the version dropdown).