Android studio gradle breakpoint No executable code found at line

I am developing an android application using Android Studio 2.1.3 and gradle.

The problem is that the breakpoint in a simple method is never hit, although it must be hit because the condition is met during application debugging.
First, I thought that the problem is related to the issue described in the answer for this question: BuildConfig.DEBUG always false when building library projects with gradle

To test this, I removed library project and integrated all my source code into the main app module. It solved nothing. To be noted that the following is the build.gradle, where minify is set to false for both debug/release:

apply plugin: 'com.android.application'  

android {  
    compileSdkVersion 23  
    buildToolsVersion "23.0.2"  
    defaultConfig {  
        applicationId "com.mycompany.mymobileapp"  
        minSdkVersion 21  
        targetSdkVersion 21  
        versionCode 1  
        versionName "1.0"  
    }  
    buildTypes {  
        release {  
            minifyEnabled false  
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'  
            debuggable true  
            jniDebuggable true  
            renderscriptDebuggable true  
            zipAlignEnabled false  
        }  
        debug {  
            debuggable true  
            minifyEnabled false  
            zipAlignEnabled false  
            jniDebuggable true  
            renderscriptDebuggable true  
        }  
    }  
    productFlavors {  
    }  
}  
  
dependencies {  
    compile fileTree(include: ['*.jar'], dir: 'libs')  
    testCompile 'junit:junit:4.12'  
    testCompile 'org.mockito:mockito-core:2.0.5-beta'  
    testCompile 'com.android.support:support-v4:23.1.1'  
    testCompile 'org.powermock:powermock-api-mockito:1.6.2'  
    testCompile 'org.powermock:powermock-module-junit4-rule-agent:1.6.2'  
    testCompile 'org.powermock:powermock-module-junit4-rule:1.6.2'  
    testCompile 'org.powermock:powermock-module-junit4:1.6.2'  
    compile 'com.android.support:appcompat-v7:23.1.1'  
}

Here is the screenshot with what Android Studio shows to me:

This is also not the only case. It happens that the compiler, while Stepping over, jumps to completely another part of the code than the one being debugged.

Is there any reasonable explanation here? Suspend: "thread" and "all" tried, same result.

UPDATE 1: Re-created the project using Eclipse, and everything works fine. It is still amazing why using Android studio this does not work!

After re-creating the application using Eclipse and observing the correct behavior, I returned to Android Studio in order to check if there is any option that I missed.

After trying all the options from File -> Settings that I could, I made the conclusion that Instant Run is the evil that caused me to waste so much precious time.

I don't understand how it is related with my problem, but after clearing all check-boxes:

I ended up with a code that executes the way I as a developer expect: