Have you tried checking under Others in Window menu? This is where less popular panels normally reside.
Align panel is an extension and there is a probability that you might have uninstalled it unknowingly.
You can follow the following steps to reinstall it:
1. Launch Extension Manager.
2. In the Extension Manager dialog, click on the "install" button.
3. Now, a dialog opens up to browse to the relevant file. You can browse to the following location:
Disk/Library/Application Support/Adobe/Fireworks/Preinstall/Align Panel.mxp
After installing the extension, relaunch Fireworks and you can see it under Windows menu.
Let me know if you have anymore issues with this.