That may be the case but I do believe I have the correct addresses as they are the only ones that are consistently counted after every battle, this would fit in with what limited prior documentation on Romancing Saga suggests too.
I still need to do more testing in r8948 to make sure that it works (going to play through an entire prologue fighting every available battle) and see if the same things happen that occurred in 1.9.2 or if it does what I'm hoping for or something else entirely.
If after the prologue I find myself locked out of early game quests and encounter significant increased enemy strength I'll assume there's more than just the battle counter that influences these things. The current documentation for Romancing Saga isn't worded well and isn't clear if the in game clock has any bearing on the issue. If results are the same in both 1.9.2 and r8948 I'll find out the addresses for the game clock and test those too along with the battle counter addresses.
I'm hoping things work out the way I want as a full fan translation of Romancing Saga is due for release soon. I'd like to try and document the game algorithms and make a guide on how certain side quests effect one another. This would be much easier if I find a way to freeze what decides to lock certain quests as the sheer amount of enemies and difficulty of avoiding them ensures you'll be locked out of quests through playing the game normally.
If there is an issue with Bizhawk though I'd be happy to help with testing specific things in a variety of games. Bizhawk has the best UI, especially so for RAM searching and watching so I wouldn't like to have to go back to Snes9x to document games.
EDIT: I suppose I should link the only site I know with any significant data on Romancing Saga so far as it might help explain my point a bit. Unfortunately it's all in Japanese but Google Translate should be good enough even though it fails to understand context.
http://www8.plala.or.jp/alice4/
And this page of the site explains a bit on the battle counter.
http://www8.plala.or.jp/alice4/74.htm#00
If the battle counter starts at 0 and counts up to 65535 as the site suggests then logically I should find the addresses that increase their values by 1 at the end of battle yes? The 4 addresses I've noted are the only addresses that do this so they should be the ones I must monitor and freeze. I will start conducting some more testing in r8948 once I get back home from work later today.
EDIT2: I have completed testing a playthrough of Albert's prologue (this one requires the most fights) in Romancing Saga using Bizhawk dev build r8948 with the addresses I've frozen. Early game side quests are available and I never encountered a stronger enemy set despite doing even more fights than my playthrough using 1.9.2. I'm convinced that address freezing does not work in 1.9.2 but does work with r8948 after this. Hopefully this info can help resolve the issue but I can do further in game testing if that's necessary, may test other games too and see if it's an issue that only effects certain games.