Thanks for your bugreport. I can confirm this problem here. The error seems to be that synaptic parses the sources.list on startup and not again before reload.
** Changed in: synaptic (Ubuntu)
Importance: Undecided => Medium
Status: Unconfirmed => Confirmed
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[feisty] Synaptic closes when changing the repositories
https://launchpad.net/bugs/84423
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