hmmm. it seems like dortmund has really a tendency to underperform, even with my sim tweaks. i might have been mistaken when i said "they're practically always top 4".
i simulated four bundesligas to check, with my settings. bayern won the league twice, wolfsburg once and schalke once. bayern finishes were 1st, 3rd, 1st, 2nd. but dortmund finishes were 7th, 2nd, 6th, 4th. a bit below par for them.
what you can do is editing the database with db master or cm. scroll to the "teams" tab and increase dortmund's domestic prestige (maximum is 20). this will force them to perform better in the simulations.
anyway, if you're having no competition in the table, you might consider increasing your difficulty level too. with the database tweak, the most you will get is bringing dortmund to the level of the teams that were chasing you before. but if the others were no competition before, dortmund won't be as well.