Could the issue be that mongo is not correctly finding the update as it is not aware of all the locations that would indicate the presence of the hotfix and the message at startup is not actually accurate?
Appl: detect Parent, Package: Package_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-WinPE-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, no parent found, go absent
Appl: detect Parent, Package: Package_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, state: Superseded
Appl: detectParent: package: Package_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7601.17514, state: Installed
Appl: detect Parent, Package: Package_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, disposition state from detectParent: Installed
Appl: Evaluating package applicability for package Package_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, applicable state: Installed
Appl: detect Parent, Package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-EmbeddedCore-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, no parent found, go absent
Appl: detect Parent, Package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, related parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7601.17514, which is not real parent
Appl: detectParent: package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, state: Superseded
Appl: detect Parent, Package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-ServerCore-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, no parent found, go absent
Appl: detect Parent, Package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-WinPE-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, no parent found, go absent
Appl: detect Parent, Package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-WinPE-Package~31bf3856ad364e35~amd64~~6.1.7601.17514, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, no parent found, go absent
Appl: detect Parent, Package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, disposition state from detectParent: Superseded
Appl: Evaluating package applicability for package Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, applicable state: Superseded
EvaluateApplicability, package: Package_for_KB2731284_RTM~31bf3856ad364e35~amd64~~6.1.3.0, Package applicability: Superseded.
Appl: detect Parent, Package: Package_for_KB2731284_SP1~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-EmbeddedCore-Package~31bf3856ad364e35~amd64~~6.1.7601.17514, Disposition = Staged, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284_SP1~31bf3856ad364e35~amd64~~6.1.3.0, no parent found, go absent
Appl: detect Parent, Package: Package_for_KB2731284_SP1~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7601.17514, Disposition = Staged, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_for_KB2731284_SP1~31bf3856ad364e35~amd64~~6.1.3.0, related parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, which is not real parent
Appl: detectParent: package: Package_for_KB2731284_SP1~31bf3856ad364e35~amd64~~6.1.3.0, parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7601.17514, state: Installed
Appl: detect Parent, Package: Package_for_KB2731284_SP1~31bf3856ad364e35~amd64~~6.1.3.0, disposition state from detectParent: Installed
Appl: Evaluating package applicability for package Package_for_KB2731284_SP1~31bf3856ad364e35~amd64~~6.1.3.0, applicable state: Installed
Appl: detect Parent, Package: Package_5_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, Parent: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, Disposition = Detect, VersionComp: EQ, ServiceComp: EQ, BuildComp: EQ, DistributionComp: GE, RevisionComp: GE, Exist: present
Appl: detectParent: package: Package_5_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7600.16385, state: Superseded
Appl: detectParent: package: Package_5_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, parent found: Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~6.1.7601.17514, state: Installed
Appl: detect Parent, Package: Package_5_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, disposition state from detectParent: Installed
Appl: Evaluating package applicability for package Package_5_for_KB2731284~31bf3856ad364e35~amd64~~6.1.3.0, applicable state: Installed