When I start Indesign, the only window pane I see is the application bar, but it only takes up half the screen. When I toggle through the workspace presets, nothing changes or appears. If I choose to show a specific window pane such as "layers", it appears in the center of the screen but is stacked with a bunch of other random window panes (but in a way unlike you would normally see when you drag a window into another, they are lieterally inside one another). I can however, drag them out and rearrange them, but when I relaunch ID, the same problem appears. I've tried trashing the prefs to no avail. Any ideas?
have you tried the Reset <workspace name> command?
if that works to rearrange the panels properly, and it doesn't stick, then you probably have a conflict with some other software. Any third party plugins? Background utilities?