Gulp-filter in one stream not delivering all files to dest

In gulp I am currently trying to copy, move and apply plugins to a bunch of src files for a build process. Try using gulp-filter to split the required files for each step and apply the correct plugins for each, it works, but only for some files.

The problem Im get is the final output in "dist" only partially showing uploaded files. I.E. its only showing css and img folders and only half of the images and also only half of the lib were all pulled. Sure enough this isn't one of the plugins failing. Also sometimes it was not completely recursive in src files.

Tried removing steps steps like image plugin but still had the same problems.

This is ideal what I want to use (and currently use, but has these problems):

var sourceFiles = [
    '!./js/_src',
    './js/**',
    './css/**/*.css',
    './img/**',
    './files/**',
    '!./login/_src',
    './login/**'
]
gulp.task('build',['clean'], function(){

    var replaceVersion = [/%version/gi,'v=' + p.version ];

    var filterHTML  = filter('**/*.html');
    var filterJSON  = filter('**/*.json');
    var filterENV   = filter('**/env.js');
    var filterIMG   = filter('img/**/*.*');

    gulp
        .src(sourceFiles, {base: './'})

        .pipe(plumber({
            errorHandler: onError
        }))

        .pipe(filterHTML)
            .pipe(replace([replaceVersion]))
            .pipe(minifyhtml())
        .pipe(filterHTML.restore())

        .pipe(filterJSON)
            .pipe(minifyjson())
        .pipe(filterJSON.restore())

        .pipe(filterENV)
            .pipe(replace([replaceVersion]))
        .pipe(filterENV.restore())

        .pipe(filterIMG)
            .pipe(imagemin({
                progressive: true,
                svgoPlugins: [{removeViewBox: false}],
                use: [pngcrush()]
            }))
        .pipe(filterIMG.restore())

        .pipe(gulp.dest(paths.dist))

        .pipe(notify({
            title: 'Gulp BUILD Success 😃',
            icon: path.join(__dirname, '/_assets/gulp.png'),
            onLast: true,
            wait: true
        }));

}); 

      

        
        
        
      

    

And this is a dirty / dirty / long breeze that I am currently solving until I find a solution:

gulp.task('build', function(){

    console.log('----------------------------------------------------');
    console.log('                     v'+ p.version);
    console.log('----------------------------------------------------');

    setTimeout(function(){ // few seconds delay to display message above

        runSequence(
            [
                'clean'
            ],
            [
                'build:index',
                'build:styles',
                'build:files',
                'build:icons',
                'build:scripts',
                'build:libs',
                'build:templates',
                'build:resource',
                'build:img',
                'build:login',
                'build:signup',
                'build:recommend'
            ],
            [
                'build:setVersion'
            ],
            [
                'build:compressHTML',
                'build:compressJSON',
                'build:compressIMG'
            ],
            function(){
                console.log('Build Complete');
            }
        )

    }, 3000)

});

gulp.task('build:index', function(){
    return gulp
        .src(['index.html'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:styles', function(){
    return gulp
        .src(['css/**/*.css', 'css/maps/*.*'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:files', function(){
    return gulp
        .src('files/**/*.*', { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:icons', function(){
    return gulp
        .src('icons/**/*.*', { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:scripts', function(){
    return gulp
        .src([‘js/app.min.js', 'js/env.js', 'js/main.js', 'js/maps/app.min.js.map'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:libs', function(){
    return gulp
        .src(['js/lib/**/*.*','!js/lib/_src/**'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:templates', function(){
    gulp
        .src(['js/templates/**/*.*'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:resource', function(){
    return gulp
        .src(['js/resource/*.*'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:img', function(){
    return gulp
        .src(['img/**/*.*'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:login', function(){
    return gulp
        .src(['login/**/*.*' ,'!login/_src/**'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:signup', function(){
    return gulp
        .src(['signup/**/*.*' ,'!signup/_src/**'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});

gulp.task('build:recommend', function(){
    return gulp
        .src(['recommend/**/*.*' ,'!recommend/_src/**'], { base: './'})
        .pipe(gulp.dest(paths.dist));
});


gulp.task('build:setVersion', function(){
    return gulp
        .src([paths.dist + 'index.html', paths.dist + '/**/*.html', paths.dist + '/**/env.js'], { base: './'})
        .pipe(replace([version]))
        .pipe(gulp.dest('.'));
});


gulp.task('build:compressHTML', function(){
    return gulp
        .src([paths.dist + '/**/*.html'], { base: './'})
        .pipe(minifyhtml())
        .pipe(gulp.dest('.'));
});

gulp.task('build:compressJSON', function(){
    return gulp
        .src([paths.dist + '/**/*.json'], { base: './'})
        .pipe(minifyjson())
        .pipe(gulp.dest('.'));
});

gulp.task('build:compressIMG', function(){
    return gulp
        .src([paths.dist + '/img/**/*.*'], { base: './'})
        .pipe(imagemin({
            progressive: true,
            svgoPlugins: [{removeViewBox: false}],
            use: [pngcrush()]
        }))
        .pipe(gulp.dest('.'));
});