The thing about winding by hand is that it is actually a circular twisting motion. When a skein is wound into a cake using a swift and a ball winder, the yarn isn't actually twisted any further.

Did you ever use a yo-yo? If you want the twist on your yo-yo to stay loose for sleeping, you can't hold the yo-yo in one hand and wrap the string around it with the other. That messes with the twist. This is the same principle.

I honestly have no idea what happened in this case. I do know that the way I knit can affect the twist of the yarn. Knitting continental supposedly increases twist, and thrown knitting supposedly decreases it. It's the opposite for me.

This particular yarn looks like it might be inconsistently twisted for a certain look. That's also a possibility.

As for the amount of yarn needed for a scarf, did the people at your LYS tell you what needles to use and how many stitches? Those affect the amount of yarn you need.

Also, I always knit from the middle of the ball (unless it has no animal fibre [except silk] at all, in which case it doesn't have enough texture to hold its shape and turns into a mess). As long as it's not wound too tightly, it'll go fine.