Exactly. So the problem could be that the editor doesn't save the SGL option in the 12.08, or it could be the game that read the 12.06 and the 12.08 differently, and wronlgy for 12.08
I have looked into the matter, and can report that the error appears to be in the editor, and that is definitely IS possible to make a BIQ version 12.08 with scientific leaders enabled and default game rules/victory conditions/etc. NOT enabled. The attached .biq is an example. I'll finish my explanation on an edit of this post, so Steph doesn't have to keep looking.
To figure out if it was possible, I saved a blank scenario with default rules but not default player data. I then disabled default victory conditions and default game rules within the Scenario tab embryodead mentioned in post #167. This can all be verified by opening up the attached .biq in Civ3ConquestsEdit version 1.03. I then opened up the file in a hex editor, and went to the four bytes where victory conditions and rules are set in binary (an explanation of the BIQ layout can be found
here at Apolyton). I noticed there are 18 items under the "Rules" section for a Civ3 game on the screen where you choose who you are playing. That is two too many for the first two bytes that are documented at Apolyton. Reverse Capture the Flag and Scientific Leaders are the two odd ones out. So I turned on Reverse CTF and saved. That changed the third byte from 00 to 02 in the hex editor. From there it was just trying all the different possibilities for that position. And it turns out, three combinations allow scientific leaders:
00 = Neither
01 = Neither
02 = Reverse CTF
03 = Reverse CTF
04 = Reverse CTF
05 = Reverse CTF
06 = Both Reverse CTF and Scientific Leaders
07 = Both
08 = Neither
09 = Neither
0A = Reverse CTF
0B = Reverse CTF
0C = Scientific Leaders
0D = Scientific Leaders
0E = Both
0F = Both
10 = Neither
16 = Both
20 = Neither
And the values of these numbers in binary, remembering Civ3 uses little-endian integers:
00 = 0000 0000 (little)
01 = 1000 0000 (little)
%02 = 0100 0000 (little) <-- this is the value used for ReverseCTF by Civ3ConquestsEdit v1.03
%04 = 0010 0000 (little)
%05 = 1010 0000 (little)
*%06 = 0110 0000 (little)
07 = 1110 0000 (little)
08 = 0001 0000 (little)
09 = 1001 0000 (little)
0A = 0101 0000 (little)
0B = 1101 0000 (little)
*0C = 0011 0000 (little)
*0D = 1011 0000 (little)
0E = 0111 0000 (little)
0F = 1111 0000 (little)
10 = 0000 1000 (little)
*%16 = 0110 1000 (little)
20 = 0000 0100 (little)
Percent signs are Reverse CTF; asterisks are scientific leaders. The attached file has value 0C in hexadecimal for this byte, and thus has only scientific leaders enabled.
The unfortunate thing is there doesn't seem to any pattern in the bits where one bit being enabled turns reverse CTF or scientific leaders on or off, as there are for the properties documented at Apolyton. But by using specific values of those listed above for each of the three possibilities for those bytes, a custom editor could allow scientific leaders with BIC 12.08.
I have not tested these values in game, to see if there are any unintended side effects. However, the attached file does at least start a game properly, and "Enable Scientific Leaders" does show up in blue on the scenario Rules on the page where you choose who you are playing.
The bit in question is number 0x376 in binary in this file (position will vary by BIQ). Version number can be verified by examining the 4-byte integers starting at positions 0x018 (major number version; reads 12 in decimal), and 0x01C (minor version number, reads 8 in decimal). You'll have to use a hex editor to verify the version numbers, unless there's some way to in Civ3ConquestsEdit/Civ3Conquests that I don't know about, as it appears Steph's editor doesn't support uncompressed BIQ's without custom rules enabled yet (this holds true for another scenario I saved just now with only Custom Game Data, not Custom Rules, enabled).