Each hotfix includes all of the original files except for changes introduced by all of the previous hotfixes. The latest hotfix contains only changes incorporated since the hotfix immediately preceding it.
In other words, hotfix 09 has exactly what my master files read this very moment, except I play from those files directly, not from a fresh Japanese ROM that has been modified by my latest hotfix IPS.
Stated yet another way, hotfix 09 is the same IPS we would release in a revision if we chose to have nine revisions at this point instead of nine hotfixes.
What I will now do for a short time only is provide you all with my up-to-date SMC. What I suggest you do is create a separate "SSMS Test" folder and put my SMC in it. Then, bring over only your advanced level battery saves (SRMs) to that test folder. Load one of your SRMs that is modified to share the same prefix name as my SMC (or rename everything to whatever you want to call it) and travel to the places you want to test.
If you still see discrepancies, let me know. First, I will re-check my saved files. If those read correctly, I will then try to test my changes again with my own saves.
Don't panic. One way or another, we'll all get on the same page eventually. This happened to us a lot in Feda, in which we had duplicate strings in different blocks that got triggered randomly through processes we never sorted out. I just searched on identical Japanese in different blocks and standardized the English insertions. We like to have never straightened Feda out, but we did, finally!
I don't believe this is the problem in SSMS, however. If several of you could test my SRM with your saves and compare results, that might be revealing.
Good luck!
http://www.dynamic-designs.us/shellmonsterstory/DKM.smc