I've updated the units to 1.07 (as displayed on the cuecore2).
I have more testing to do, but it still doesn't seem to be fading between cues. I've moved away from timers as before the firmware update, the timer transport controls were really finicky and the stop command didn't work. I didnt try it again after the update. (I'm thinking that my unit had a bad flash of the original firmware, it was really buggy all around)
Right now I have a timer of sorts built into the playback 1. For three minutes it runs cue 1, then runs cue 2 for 27 minutes to complete a thirty minute cycle. Even both cues have a 5s fade time, it still is jumping between cues. I'll test it more tomorrow when I have more time and its darker out. I've moved away from timers due to the nature of being able to trigger them. With no logic or the ability to have more advanced time controls, timers in this scenario don't work well for me.
Thanks