Thank you for your post, and I apologize for the late reply.
I am unable to replicate the problem with either FileMaker Pro 11.0v3 or FileMaker Pro 11.0v4. These are the steps I took:
1. I created a new database file.
2. I created a simple script, duplicated it 30 times, and I was able to select the last script and drag it upwards to a new position.
3. I duplicated the Layout 30 times, and I was able to select the last layout and drag it upwards to a new position.
Let me know what I'm doing differently than you, and I'll try it here.
I think this problem was addressed in the latest Update.
At least it disappeared since then.