Weird sourcemap behavior

gulpfile.js

var gulp = require('gulp');
var gutil = require('gulp-util');
var browserify = require('browserify');
var watchify = require('watchify');
var notify = require("gulp-notify");
var buffer = require('vinyl-buffer');
var globby = require('globby');
var source = require('vinyl-source-stream');
var sourcemaps= require('gulp-sourcemaps');
var through= require('through2');
var reactify = require('reactify');
var uglify = require('gulp-uglify');
var ifelse = require('gulp-if-else');
var less = require('gulp-less');
var autoprefixer = require('gulp-autoprefixer')

//var bundleLogger = require('../util/bundleLogger');
//var handleErrors = require('../util/handleErrors');

var config = {
    // Enable source maps
    debug: true,
    extensions: ['.jsx'],
    // A separate bundle will be generated for each
    // bundle config in the list below
    bundleConfigs: [ 'app'],

    srcFolder: './Scripts/Jsx/',
    destFolder: './Scripts/'
};

var handleErrors = function () {
    var args = Array.prototype.slice.call(arguments);
    // Send error to notification center with gulp-notify
    notify.onError({
        title: "Compile Error",
        message: "<%= error.message %>"
    }).apply(this, args);

    // Keep gulp from hanging on this task
    this.emit('end');
};

function doBrowserify(callback) {

    var bundleQueue = config.bundleConfigs.length;

    var browserifyThis = function (entry) {

        var reportFinished = function () {
            // Log when bundling completes
            //bundleLogger.end(bundleConfig.outputName);
            //console.log(bundleConfig.outputName);

            if (bundleQueue) {
                bundleQueue--;
                if (bundleQueue === 0) {
                    // If queue is empty, tell gulp the task is complete.
                    // https://github.com/gulpjs/gulp/blob/master/docs/API.md#accept-a-callback
                    callback();
                }
            }
        };

        var minify = function() {
            var stream =  through({objectMode:true})
            stream
                .pipe(sourcemaps.init().on('error', gutil.log))
                .pipe(uglify())
                .pipe(sourcemaps.write("./"));
            return stream;
        };

        var bundledStream = through({objectMode:true});
        bundledStream
            // Report compile errors
            .on('error', handleErrors)
            .on('end', reportFinished)
            // Use vinyl-source-stream to make the
            // stream gulp compatible. Specifiy the
            // desired output filename here.
            .pipe(source(entry + '.js'))
            // Specify the output destination
            .pipe(buffer())
            .pipe(ifelse(!config.debug,function() {return sourcemaps.init()}))
            .pipe(ifelse(!config.debug, uglify))
            .pipe(ifelse(!config.debug,function() {return sourcemaps.write("./")}))
            //.pipe(ifelse(!config.debug, minify))
            .pipe(gulp.dest(config.destFolder));


        globby([config.srcFolder + "main.js"], function(err, entries) {
            // ensure any errors from globby are handled
            if (err) {
                bundledStream.emit('error', err);
                return;
            }

            // create the Browserify instance.
            var b = browserify({
                entries: entries,
                //basedir: config.srcFolder,
                debug: true,
                transform: [reactify]
            });

            // pipe the Browserify stream into the stream we created earlier
            // this starts our gulp pipeline.
            b
            .exclude('react')
            .exclude('d3')
            .bundle()
            .pipe(bundledStream);

        });

        return bundledStream;
    };

    // Start bundling with Browserify for each bundleConfig specified
    config.bundleConfigs.forEach(browserifyThis);
}

gulp.task('browserify', doBrowserify);

gulp.task('watch', function () {
    gulp.watch(['./Scripts/Jsx/**/*.jsx', 'Scripts/Jsx/*.js'], ['browserify'], function () {

    });

});


gulp.task('default', ['browserify'], function () {
});

gulp.task('release', function (callback) {
    config.debug=false;
    return doBrowserify(callback);
});