This has been repeatedly reported in this forum. You might search out some of the other discussions to see what can be learned about this issue.
With FMP Advanced 16 if you are in a long script using the script debugger it automatically jumps ahead. For example, if you are in line 45 and you have scrolled ahead to see what is coming up, when you click to line 46 the active line becomes the last line and you can no longer see what is next.
This is new in 16. Is there any way to correct this behavior?
Wait for the patch.