i confirm this is happenning here to in Jaunty 9.04.
Actually it just deletes the 3rd party source listing from the UI while the
/etc/apt/sources.list is edited correctly (using #)
** Changed in: software-properties (Ubuntu)
Status: New => Confirmed
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Unticking in software-properties-gtk will mistakingly delete 3rd party sources
https://bugs.launchpad.net/bugs/324614
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