Strange one,
,
Are you sure your satellites.xml file has been reloaded along with your bouquets? Maybe DBEdit is uploading it to the wrong place in the new image.
I've had problems before when I imported bouquets from pet settings to my own config. Because Thor was listed as 1W in pet settings, but Thor was 0.8W in the default satellites.xml in the newly flashed image I had problems.
Result: Confused box.
I'd be focusing on the satellites.xml file to start with. Especially since you say there are no transponders listed for certain sats.
Did you try setting up GotoX then scanning a sat with a freshly installed image, before loading your channel list with DBEdit, ? Might be worth a shot, It could give you a hint as to whats wrong.
Good Luck
EDIT: PS the services file will also cause problems if there is a mismatch between it and other necessary files.
PPS: I've always found Dreambox Control Centre to be much better for backing up and restoring bouqets/channel lists because it autodetects the correct directories to use. Its no use for editing channels etc but handles restoring in a better way. You could attempt to use DCC to restore the channel lists saved by DBEdit, just point it to the correct directory then click restore, You've got nothing to lose.