I think I found the files. They are the keyboard profile files in ~/Library/Preferences/Parallels/.
The MouseShortcuts in my Windows profile looks like this (I think you just need to set enable to 0?):
	Code:
	
   <MouseShortcuts dyn_lists="MouseShortcut 2">
      <MouseShortcut id="0" dyn_lists="KeyCombination 1">
         <Enable>0</Enable>
         <MouseButton>1</MouseButton>
         <MouseButtonShortcut>0</MouseButtonShortcut>
         <Delay>0</Delay>
         <KeyCombination id="0" dyn_lists="">
            <UseAlt>0</UseAlt>
            <UseCtrl>1</UseCtrl>
            <UseCmd>0</UseCmd>
            <UseShift>1</UseShift>
            <CustomKey>0</CustomKey>
         </KeyCombination>
      </MouseShortcut>
      <MouseShortcut id="1" dyn_lists="KeyCombination 0">
         <Enable>0</Enable>
         <MouseButton>1</MouseButton>
         <MouseButtonShortcut>0</MouseButtonShortcut>
         <Delay>3000</Delay>
      </MouseShortcut>
   </MouseShortcuts>