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>