Since a few days, i have the same problem !! 
after i hit the off button, and then i choose the good activity, my harmony smart control doesn't reconnect itself. 
I see the message "press any key to connect Harmony" but when i press a key nothing happens.

if i re-syncronise it, my harmony works well, but that takes 1 or 2 minutes each times.

I follow all FAQ : 
- battery OK 
- no power options 
- no soft keyboard pairing 
- Bluetooth turned on

Thanks a lot for a solution or an explaination