Hi, thanks for the comments. The interface is different form EDIE/EDEE and does take some getting used to.
For some of the comments:
"Wait" moves your unit to the end of the processing queue. Activate Last will activate the unit previously active. Be aware that this includes units that may have been automatically processed, not just units you manually interacted with.
There is a Launch command button. It will be in the command button group (bottom buttons). If you do not see it, you may not have this section open all of the way.
The reports dialog does close upon choosing a report. All reports can be bound to a key, so if there is a report you frequent, I would recommend setting that up.
The extra reports message is a bug that has not yet been addressed.
If you mouse over an enemy spot, the info box in the lower right will list the age of the spot.
"Prep Unload" should be used when you have a transport you wish to move and then unload. If you need a prep load, "Load Till Full" may satisfy that, otherwise use load instant.
There is a right click menu option which can be used for activating a unit, but there is not a select via right click option.