It looks like your io.vertx.core.impl.IsolatingClassLoader actually has both the specific module and the global module added to it as URLs:
2018-01-17T12:33:20.234+0100 FastClasspathScanner ------ Finding classpath elements in ClassLoader io.vertx.core.impl.IsolatingClassLoader@5ae058df
2018-01-17T12:33:20.235+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/com/ernestojpg/specific-module/1.0-SNAPSHOT/specific-module-1.0-SNAPSHOT.jar
2018-01-17T12:33:20.235+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/vertx/vertx-core/3.5.0/vertx-core-3.5.0.jar
2018-01-17T12:33:20.235+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-common/4.1.15.Final/netty-common-4.1.15.Final.jar 2018-01-17T12:33:20.235+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-buffer/4.1.15.Final/netty-buffer-4.1.15.Final.jar 2018-01-17T12:33:20.235+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-transport/4.1.15.Final/netty-transport-4.1.15.Final.jar
2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-handler/4.1.15.Final/netty-handler-4.1.15.Final.jar 2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-codec/4.1.15.Final/netty-codec-4.1.15.Final.jar 2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-handler-proxy/4.1.15.Final/netty-handler-proxy-4.1.15.Final.jar
2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-codec-socks/4.1.15.Final/netty-codec-socks-4.1.15.Final.jar
2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-codec-http/4.1.15.Final/netty-codec-http-4.1.15.Final.jar
2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-codec-http2/4.1.15.Final/netty-codec-http2-4.1.15.Final.jar
2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-resolver/4.1.15.Final/netty-resolver-4.1.15.Final.jar
2018-01-17T12:33:20.236+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-resolver-dns/4.1.15.Final/netty-resolver-dns-4.1.15.Final.jar
2018-01-17T12:33:20.237+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/netty/netty-codec-dns/4.1.15.Final/netty-codec-dns-4.1.15.Final.jar
2018-01-17T12:33:20.237+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.9.0/jackson-core-2.9.0.jar
2018-01-17T12:33:20.237+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/com/fasterxml/jackson/core/jackson-databind/2.9.0/jackson-databind-2.9.0.jar
2018-01-17T12:33:20.237+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/com/fasterxml/jackson/core/jackson-annotations/2.9.0/jackson-annotations-2.9.0.jar
2018-01-17T12:33:20.237+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/.m2/repository/io/github/lukehutch/fast-classpath-scanner/2.9.4/fast-classpath-scanner-2.9.4.jar
2018-01-17T12:33:20.237+0100 FastClasspathScanner -------- Found classpath element: /Users/eperez/Development/NetBeansProjects/fast-classpath-scanner-test/global-module/target/global-module-1.0-SNAPSHOT.jar
In the log, the scanner correctly does not ask the parent classloader sun.misc.Launcher$AppClassLoader for URLs. So in your case, the fix would be to make sure that the global module is not in the URL list for io.vertx.core.impl.IsolatingClassLoader.
However, your log brings up another interesting issue -- ignoring parent classloaders won't work if the parent classloaders' entries are also in java.class.path, since any paths found there will always be scanned. From the log, you can see that the global module was found in both IsolatingClassLoader and java.class.path:
I probably need to always fetch all URLs from all classloaders, then if parent classloaders are disabled, remove any URLs from java.class.path that are in parents but not in the child. This still wouldn't fix your situation though, since both module URLs are in the child classloader.