Oddly enough:
/etc/ssl/certs/UbuntuOne-Go_Daddy_CA.pem
        Issuer: C=US, O=The Go Daddy Group, Inc., OU=Go Daddy Class 2 
Certification Authority
        Subject: C=US, ST=Arizona, L=Scottsdale, O=GoDaddy.com, Inc., 
OU=http://certificates.godaddy.com/repository, CN=Go Daddy Secure Certification 
Authority/serialNumber=07969287

/etc/ssl/certs/UbuntuOne-Go_Daddy_Class_2_CA.pem
        Issuer: C=US, O=The Go Daddy Group, Inc., OU=Go Daddy Class 2 
Certification Authority
        Subject: C=US, O=The Go Daddy Group, Inc., OU=Go Daddy Class 2 
Certification Authority

so the intermediate cert is there, but is considered a duplicate.

Also, the target host should be fixed to serve the intermediate CA.

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https://bugs.launchpad.net/bugs/855454

Title:
  Breaks some roots

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