I use Progression 3 with no Problems entering chords.

Over teh fretboard select the chord symbol and then select the pencil symbol. Then draw your chord and press enter. The chord should now be displayed in the staff.

Yep..
* You gotta click the Pencil icon to enter Edit mode.
* Then the chord button.
* Then the fretboard to structure the chord.

Then you gotta click the top of the Guitar staff where you want to place the chord.
A VERY small silhouetted circle will appear inside the cursor (the light yellow shaded playback cursor.. that's what I call it).
Then hit Enter.