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You really ought to contact the OmniPlan support ninjas via Help->Send Feedback (which will allow you to attach a copy of your project file with the sensitive information obscured). That's the only way to make sure that someone who knows the ins and outs of the program sees it in a timely fashion. I don't have any MP experience, nor a copy of it to play with, so I can't really offer any suggestions.

If you have dragged things around on the OmniPlan Gantt chart, that schedules specific start dates for those tasks rather than letting them fall where the constraints would otherwise allow. If you select all the tasks in your project and click the Reset button in the Task Information inspector to set them all to be scheduled as early as constraints allow, then export to MP, does the resulting document work properly (ignoring any issues about how some things aren't starting at the right time because you didn't have fixed dates for them in OP)? Not proposing this as a solution, just a way to get a start on isolating the problem, of course...