Problem with Monomer puzzles, Primary Structure (PS)/segment counts

I don't know what causes these discrepancies, but I've noticed that I sometimes get incorrect results from using a utility script that I've used for years to read/write primary/secondary puzzle strings. The common thread seems to be that it only happens with Monomer design puzzles since the ability to add/delete segments was implemented. 

Take for example Puzzle 1260 (85 segments). I definitely deleted/added, or added/deleted single segments to end up with the correct number of segments (85). The script is: 

"AA Copy Paste Compare v 1.1.1 -- Brow42"    (http://fold.it/portal/recipe/38147)

I've used this script for years to read/write and copy/paste primary and secondary structures.

I have tested the script by starting puzzle 1260 on a computer in an unaltered default track. The read/write functions for the PS appears to work flawlessly, as I can switch between all isoleucines and alanines without any problem. Even after adding/deleting segments (in different places). 

However, several times over many different monomer puzzles, I have noticed that the script doesn't function correctly at later stages of the puzzle. For example, I have shared an instance with scientists: "gw10495.716 solo".

To replicate the problem:

   1. load "gw10495.716 solo"
   2. start script "AA Copy Paste Compare v 1.1.1 -- Brow42"    (http://fold.it/portal/recipe/38147)
   3. click "read", then "read" again.

The results show that it reads from range 1 to 84 (not 85) and the sequence omits segment 85 (glycine) in the results. However, if you use the tab key on the first and last segments, the client will display numbers 1 and 85 (glycine) respectively. Is there possibly a pointer missing somewhere for segment 85 that throws the script off?

The result is that the script can no longer modify structures on this saved puzzle. So my concern is what other scripts am I using that might be affected by issues related to this problem? Is the last segment being ignored during processing?