You're right, the lines you have are from an older version, v12 I believe when a bunch of "fixes" were made, but were temporary fixes, there were a few from members here that I, other members or Maruno fixed... How the hell they made it in to this game is beyond me, maybe it was part of my scripts that I neglected to check since the game works perfectly fine otherwise.
Edit these lines from the scripts accordingly, since I found other things too:
PokeBattle_Battler;
Remove Line 645.
Add return to Lines 176 and 181.
Remove Lines 223-225 or Add $DEBUG && after the if (not a problem but you won't want these lines when a game release comes).
Remove the (1)# on 264 to make this work as intended.
Add return false to line 2045. (I forgot to mention when I made that script that you need to specify whether it should work or not).
Add user.pbReduceHP(damage) to line 2251.
PokeBattle_ActualScene;
Remove # from line 1688 (not game effecting just nit-picky things).
PokeBattle_Pokemon;
Remove the return on Line 248 (not game breaking, since this isn't implemented yet, but return is not the right thing for this part).
Line 821, you can remove the whole line (just not needed to be honest).
Lines 1022, 1024, 1026, 1028 and 1030 all need !=nil added to the end (just a precaution).
That is all I found, none of these are game breaking really which is how you never found them until your Leech Seed problem... I think I'm going to send you the Scripts file instead of messaging you the scripts from now on (which is longer and I don't have time to do this with all little scripts) because you are not following instructions properly or your not adding the scripts fully.
Just so we're clear, this should not be added to anyone else's game, they won't fix any of your problems lol.