The best place to get answers to data file questions is at 
http://groups.yahoo.com/group/pcgen where many expert Data Monkeys hang out. 
 
That said, I think I can figure out what's going on....
In the Settings menu, click on Preferences.  In the left-hand window select "Monsters".  Make sure the "Use Default Monsters" option is checked - that's what will actually make use of the HITDICE: tag.  Having multiple HITDICE: tags is not a problem - PCGen will use the last one and ignore any previous ones.  The LANGAUTO: tag uses a | delimiter, not a comma.  A good way to see if you're getting any errors is to bring up the Console from the Debug menu (you don't need to be in Debug Mode) before you load your sources.  Exceptions and other kinds of errors get sent there and might be helpful.  Make sure you have tabs between all your tags - just spaces would cause a problem.  There used to be a problem if you had a space before or after a tab, but that shouldn't be an issue anymore, though we still tell everyone to make sure that they only use tabs between tags. 
 
Maybe Tir or one of the Data Monkeys who are more experts on the races could give you a better explanation, but you'll notice that I added a MONSTERCLASS: tag and TYPE:.  I think those are necessary when using the Default Monster option to have the HITDICE automatically added - PCGen needs to know what kind of hit die its tied to class-wise (Animal is a class!).  Here's what I had and it seemed to work properly:
Saurial Flyer	FAVCLASS:Rogue	STARTFEATS:2	MFEAT:Scent	SIZE:S	MOVE:Walk,20,Fly,50	REACH:5	HEIGHT:M:32

4:0:F:30

4:0	WEIGHT:M:30

1:F:25

1	AGE:20

4

6

6	CHOOSE:LANGAUTO:Common|Draconic	LANGBONUS:Sylvan,Elven,Celestial	BONUS:CHECKS|BASE.Reflex|3	BONUS:COMBAT|AC|4|TYPE=NaturalArmor.REPLACE	BONUS:COMBAT|BAB|1	LEVELADJUSTMENT:2	RACENAME:Saurial Flyer	HITDICE:2,8		SKILLMULT:1	MONSTERCLASS:Animal:2	TYPE:Animal		VISION:Low-light	CSKILL:Craft|Diplomacy|Jump	BONUS:SKILL|Climb,Jump,Move Silently,Listen|2|TYPE=Racial	BONUS:SKILLRANK|Hide|4	BONUS:STAT|CHR|-2	BONUS:STAT|CON|-2	BONUS:STAT|DEX|4	BONUS:TOHIT|TYPE=THROWN|1	BONUS:TOHIT|TYPE=MELEE|1	MONSTERCLASS:Humanoid:2	SA:+3 to reflex saves	SA:+4 size bonus to Hide checks	SA:Scent(Ex)	SA

rotection from Sonic Attacks +4(Ex)	SA:Vulnerability to Gas Attacks -4(Ex)	SA:Cold Torpor	CR:2	TYPE:Humanoid	SOURCEPAGE: Dragon 292 p37	NATURALATTACKS:Claw,Weapon.Natural.Melee.Piercing.Slashing,*2,1d3|Tail,Weapon.Natural.Melee.Bludgeoning,*1,1d2
Let me know if this works for you!
Bryan McRoberts
Code Monkey Publishing, Co-Founder
Benevolent Dictator of PCGen
p.s. welcome to the world of editing lst files!  Your first try is very impressive! Post a message on our yahoo board if you'd like to dabble with our data files - we're always looking for more monkeys!  Put "Tir! Reap my soul!" in the subject, and Tir will know to contact you. 

  We're slowly adding more editors within PCGen (right now we have an editor for Deities and Skills, and next will be Spells) which should make the data monkeys jobs much easier. As you can see, the lst file syntax is a bit arcane, but certainly not insurmountable. 
