ALT+tab will switch between separate application windows - or separate instances of applications running.
CTRL+tab will switch between windows in the same applications (typically this applies to an MDI - multi document interface). e.g., if you open two projects while the application is already running, then the same 'host' application is servicing them both. You would use ctrl+tab to flip between them. This same this thing happens on a 'tabbed' browser. The ctrl+tab will move between each tab. (this is also and MDI interface - just displayed as tabs).
I think you can control this in CbB by selecting the open each project in a new window (or something like that). If the application doesn't 'force' a new instance of the application (alt+tab), then it is running in the same memory space (ctrl+tab) to switch what has 'focus'.
Good luck!