Difference between running lint via Android Studio menu and gradlew command-line

You are running two different tools. The command:

$ ./gradlew lint

runs the lint tool that comes with the Android SDK and the menu option

Analyze->Inspect Code...

in Android Studio is a feature inherited from JetBrains IntelliJ IDEA which runs:

<android studio path>/bin/inspect.sh

In Android Studio you can customize what inspections are run via Preferences > Inspections; you may have some Lint inspections disabled, and not all run by default. Android Studio can also run a great number of non-Lint inspections.