Hello Danit,
I expect that the track which is save in the CueCore2 includes the fade in time. When you dump a cuelist from CueluxPro to the CueCore2 it will include the fade in time. If you do not want the fade in time saved in the CueCore2 you will have to start the playback in CueluxPro before you dump it.
About the flashing static scene. I assume that you have created a playback in the CueCore2 which plays your static scene. This playback contains one cue with the track. I assume that you want to have this static scene played forever. Which you can do by setting the duration of the cue to "forever". If you have done that your static scene should not flash.
If I have misunderstood your problem, it could be helpful to send your backup files or video.
Best regards,
Guido