I think this is a bit misunderstood. 3rd place teams get promoted through the play-offs roughly as often as you would expect. There's no hoodoo on 3rd place, if anything they actually win slightly more often than you'd expect on form/stats alone.
In the Championship, since play-offs began:
3rd - has won it 36% of the time
4th - has won it 25% of the time
5th - has won it 25% of the time
6th - has won it 14% of the time
To get these stats the base probability distribution would mean that 3rd beats 6th in the semi-final with ~65-70% probability. That is not far off the kind of odds you would have in a regular season match, possibly slightly better. Leeds play Bristol, who are 6th, at home with a larger gap between them on Monday and they only have a 78/22 edge.
Putting the stats aside though, you are right in saying there are plenty of examples of 3rd place teams who've completely bottled it. It's just that on average, that's not the case.