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Where is the ntc sensor measuring? Hot or cold side, heat sink, etc? I presume you're using a large enough 12V supply?
My suggestion would probably be to have the sensor measure the cold side of the peltier. This should then command the controller to either heat or cool that side as per the dial setting.
BTW, I have a DSII OSC with attached Peltier unit. You're welcome to borrow it if you wish. My solution in 2009 to making it work well was to put it in my cupboard and buy a QHY8
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