Applications that put the phone into Standby mode (as opposed to keylock, device lock, screen-off sleep mode, etc.) are great power saving apps BUT wreak havoc with applications, both native BB apps and 3rd party apps.
Ideally, applications that put the phone into Standby would remember the state of each and every application, save those settings, and then hibernate; and then when the standby application invokes the phone to wake up, it would read those settings and restore them.
That said, standby applications cannot be expected to even be aware of what applications are installed on every individual's phone, let alone check their state and save settings so that they can be restored upon wakeup.
Remember when Windows' much-touted Hibernation Mode was first introduced back in the day? And how when the PC was brought out of hibernation, the serial ports sometimes didn't work, mouse worked sometimes (and usually erratically), HD sometimes didn't spin up, and several of the applications that were running at the time would crash shortly after the wakeup, etc.? Eventually those issues were solved because applications were written to be more aware of hibernation, and hibernation was part of the Operating System.
While standby is something that the BB OS supports, a 3rd party application that invokes standby mode is not native in itself and probably is not aware of other running applications, and other applications are probably not aware of 3rd party applications that put the BB into standby mode.
Also, many apps that require keystroke injection cannot execute commands while the BB is locked, keylocked, in standby mode, or off. Currently there are only two Profile Scheduler apps out there, and you have the better of the two.
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BlackBerry Certified Support Specialist