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We are having a major problem with the life of our clock batteries on the Gumstix boards that we are using.
When I went back and looked at the Geppetto information on the RTC, it specifies that the RTC consists of an I2C trickle charger, a crystal, and a battery connector with part number ML-621S/ZTN.
However, when you click the link for the part number within Geppetto, it directs you to an "error" webpage for Arrow Electronics. Upon further searching, that part number turns out to be not for the battery connector, but for a Lithium Panasonic coin cell battery. This particular battery specifically states on its datasheet that trickle charging is not to be used (http://industrial.panasonic.com/cdbs/www-data/pdf/AAA4000/AAA4000PE17.pdf).
It seems like somewhere along the line, either the right parts are not specified or something was overlooked, but I thought it best just to go back to the source before hunting any further.