Viterbi Decoder - Symbol Alignment
I find it surprising that it didn't matter where you started.  Normally incorrect symbol alignment will completely change your results.  The usual method for determining the correct alignment (assuming you don't have other information like a Frame Alignment Word to help you figure it out) is to try both possible phases and see which produces a lower path metric.

You can, by the way, do the same when the code is punctured, you just have more phases to try.