Solutions
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JB's post in Help: Game won't let me test a CTR? was marked as the answerThis is just a guess, but maybe the "SuspendedSwingingBogey" (mentioned in the BahnDaten) needs to be used for a suspended coaster? I was never able to figure out how to use that piece, but it sounds like it would be necessary. I think it's the thing that attaches directly to the track, with the car(s) hanging below it. No idea how/why this would affect the station though.
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JB's post in Saved structures have items missing was marked as the answerAdding to what Bookworm said, you might try turning on transparency and seeing if the missing items have been lowered underground. You said you tried making the selection area larger, try making it considerably larger, like 5 tile widths, and try again. Hope one of these ideas will work for you.