I just moved to a new 27-inch iMac and have attached my older Cinema Display as a second monitor. When I open ID6, the document always opens on the older, smaller monitor, even though I have it set up as the secondary. PhotoShop and Illustrator don't exhibit this behavior. The only way I've found to solve this is to unplug the monitor, but then I'm giving up all this screen real estate.
Is there a setting I'm missing? Or a workaround – short of only working with one screen?
In Mavericks, each display is considered a separate "space" so both have a menu bar at the top. As such, if ID opens in the wrong display, simply move it to the other display and it should save those settings going forward. With the "spaces" feature OSX normally saves which apps open in which space.
To turn this off, you need to go to Mission Control preferences and uncheck "Displays have separate Spaces". This will put it back to the old way of 2 displays acting as one big one and should force all apps to always open in the main display first.