The active directory is the directory that the last opened file was found in. Sometimes when returning to a page after clicking on a highlighted tag, the original tag doesn't highlight until the page is moved a bit. If you zoom a master window and then command-click on a link and the slave hasn't been zoomed, the slave view won't be scrolled correctly. Implement a history mechanism. There should be some kind of visual cue about whether a window is a slave or master and if it is frozen or unfrozen.
Windows open exactly on top of each other.
This needs to be fixed. Preferences for various behaviors. Other features people ask for. Clean up the source code a bit. Clean up the source code a lot.