Callback hell.

gistfile1.js

function refresh() {
    chrome.windows.getAll(function(windows) {
        for (var i = 0; i < windows.length; i++) {
            chrome.tabs.getAllInWindow(windows[i].id, function(tabs) {
                chrome.storage.sync.get('active', function(object) {
                    if (object.active !== undefined) {
                        for (var j = 0; j < tabs.length; j++) {
                            if (-1 !== object.active.indexOf(tabs[j].url)) {
                                chrome.tabs.reload(tabs[j].id);
                            }
                        }
                    }
                });
            });
        }
    });
}

Dat way maybe?

function refresh() {

    function allWindowsCallback(windows) {
        for(var i = 0; i < windows.length; i++)
        chrome.tabs.getAllInWindow(windows[i].id, oneWindowCallback);
    }

    function oneWindowCallback(tabs) {
        chrome.storage.sync.get('active', function(object) {
            if(object.active !== undefined) for(var j = 0; j < tabs.length; j++)
            if(-1 !== object.active.indexOf(tabs[j].url)) chrome.tabs.reload(tabs[j].id);
        });
    }

    chrome.windows.getAll(allWindowsCallback);
}