Our SCM system is setup such that a number of projects in Synergy all inherit from (are child projects of) one "Master" project. To perform such builds in Jenkins, the project we are referencing is a build-user copy of the Master project (in a working state).
If someone checked in files that affect/are related to sub-projects off that Master project in Synergy, then the SCM Polling within Jenkins Synergy plugin successfully identifies that changes occurred, but the "Check for Modifications" feature prevents the build from being triggered. This appears to be because the changes did NOT directly affect members/sub-directories of the Master project, but instead of sub-projects within Master.
This would seem to be a bug, since the perceived intent of the "Check for Modifications" feature is to prevent check-ins that are to the same Synergy Release Attribute but to unrelated Synergy SCM projects from kicking off Jenkins builds of unrelated projects, but a sub-project off a "Master" is indeed related and should thus trigger a build if changes are detected.