All harmonys know the state of each device and whether it should be off or on and which input should be selected. If it's turning off devices that are needed then there are two possibilities:

1) the device is not included in the activity and the "leave unused devices on" option is not checked. Add the device to the activity in question.

2) the device is in the activity but the power control is configured incorrectly. Determine how each device controls power by going into device mode and trying any power commands (off, on, anything labeled PowerXXX) to see if you have discrete on/off commands (on always turns it on, off always turns it off) versus a power toggle (one button that toggles power on and off). Then select the Adjust Power option for the device and make sure it's setup correctly.

This is typically caused by having a power toggle setup as a discrete ON command. The remote thinks it's sending an ON command to the component (in case it was turned off for some reason) but it's really sending a toggle that turns it off.