That is by design, keep turning it. You only have three other choices.
If the engine and tranny are both out, measure the flexplate and find the one short span between holes, and mark the bad hole. repeat on the TC, and mark it. Turn the crank so that the mark is at either the 4:30 position or the 7:30 position. That is to say the marked hole ends up on either side of the pan. Rotate the TC to match.
If the tranny is to be installed after the engine is in,make sure you can see the marks from the floorside.
If the engine and tranny are already in the car and mated;
The easy way; is to orient the crank so that two flex-plate ears are are accessible. Then rotate the TC until those bottom two lugs line up.Then run one bolt in finger tight. Rotate the crank to find a third screwhole. If it lines up then spin 'em all in, you lucked in. If the third hole does not line up, back the crank up to the starting position. Remove the one bolt and rotate the convertor to the the next lug.
If those bottom two line up,put a bolt in and repeat the test.
If they don't, rotate the TC back to where you started, but continue one lug in the same direction.Install a bolt, and look for the third to line up again.
If you do this right, you will never have to turn the crank more than about 1/4 turn, and worst case is twice.
