Copy & Pasted text from PDF messes up upper-case words..

Hey there,
Have this problem on many PC's in my work, on Windows Vista and Windows 7, using Adobe Reader v9.1.0.
When highlighting text and copying, then going elsewhere and pasting, the 'case' of the text messes up.
For example, if I copied:
"The QUICK brown FOX jumps over the Lazy DOG"
The pasted text would appear:
"The QUicK brown FoX jumps over the lazy DoG"
Is this a known issue? It's doing it on different PC's with different OS's but the version of Adobe Reader is still the same, so it's either an issue with that, or with the PDF's we're reading. They are PDF's of newspapers, but still... text is text, so it shouldn't be an issue!
It's taking quite a lot of time having to scroll through all this text to make sure all the capitalization is correct (especially when it comes to grammar).
Just wondering if anyone else has come across this problem, or if there's any known solution!
Thanks in advance
-Rhydz

To copy and paste in a single action:
tell application "Preview" to activate
tell application "System Events" to tell process "Preview"
    -- Get the PubMed ID:
    get the title of the front window
    set thePubMedID to word 1 of result
    -- Copy the selected text to the clipboard:
    keystroke "c" using {command down} -- ⌘C
    delay 0.25 -- adjust if necessary
    -- Add the PubMed ID to the contents of the clipboard:
    set theNotes to the clipboard
    set the clipboard to (theNotes & space & "[" & thePubMedID & ".pdf]")
end tell
tell application "Notational Velocity" to activate
tell application "System Events"
    -- Paste the contents of the clipboard to the end of the Notational Velocity document
    key code 125 using command down -- ⌘↓
    keystroke return & return
    keystroke "v" using {command down} -- ⌘V
end tell

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