It's the same scenario at GitHub. I've had a half-dozen or so GitHub users report cert chain issues on OS X over the last year and a half and it has always turned out to be a stray cert in the 'login' keychain. Still no definitive explanation for where the cert is coming from, but in at least one case the user had been prompted to import the cert by the code signing utilities.

My understanding from DigiCert is the cross-signing with Entrust had been done awhile back to improve mobile browser compatibility. Perhaps this is some strange combination of developer tools installed and the platform they are developing for...