Sorry if my posts where coming across as bad or mean. It was NOT my intent in anyway.
Fair enough. I do appreciate your help, even if it does come with some snark. You spend more time on these boards helping us noobs more than most, so you're allowed some leeway.
When in bat form you only have a Bite so it can't be secondary by the rules (hence why HL is not making it secondary).
I get that, though natural attacks do become secondary when combined with weapon or unarmed strikes. The rules cover that possibility; it just seems that HL doesn't recognize it as a viable option the same way it doesn't allow two weapon fighting with unarmed attacks.
This would be rule argument with your DM. Because as a MoMS you have NO FoB meaning you must use Unarmed Strikes (ie Fists) to make attacks. HL is following those rules to the letter (ie only with Flurry of Blows can you make Unarmed Strikes with the rest of your body). If you and your DM agree on "house-rules" that is outside of HL. But without Flurry of Blows you need "hands" to do your unarmed strikes. I am just trying to explain why HL is doing what it is doing. Anything else would get into the area of making house-rules which you can do with special scripts in HL.
The section I quoted earlier isn't from the Flurry of Blows description; it's from the monk's Unarmed Strike description. But it isn't even a monk thing; the general weapon description for unarmed strikes is:
"An unarmed strike is always considered a light weapon. Therefore, you can use the Weapon Finesse feat to apply your Dexterity modifier instead of your Strength modifier to attack rolls with an unarmed strike. Unarmed strikes do not count as natural weapons (see Combat). The damage from an unarmed strike is considered weapon damage for the purposes of effects that give you a bonus on weapon damage rolls. Again, there's no mention or even an implication that hands are required. Now, a GM could decide unarmed strikes without fists is dumb and disallow them in his game, and that would be fine, but THAT would be the house rule.
I'll admit I may be wrong, and I'll apologize if there's some hidden hand-centric clause for unarmed strikes I've missed somewhere, but if there is it'll be news to me. ATM I'm just trying to build my character with the RAW.
If with all this you disagree on I have no horse in the race I am just trying to explain "why" HL is doing what it is doing.
I get that and I promise I won't hold you accountable for HL's failings.

I'm seeing now more and more that they way LW has setup HL is in accordance with their own interpretation of the rules (or perhaps what they perceive to be the RAI) but not necessarily in keeping with the RAW. That seems a shame to me since it limits the product and requires users to apply an increasing number of band-aid adjustments to get it to work.
HL treats Monk and Unchained Monk as two totally different 'Things' so the Unique ID of class abilities (like Flurry of Blows) don't line up and the scripts don't work.
Yeah, I imagined that's where the problem lay. A new 'thing' was created for the Unchained Monk's FoB. So I'd have to create a copy of the MoMS archetype and switch it over to the new 'thing' designation to get it to recognize what it's supposed to replace. Doable, just more work.
Unfortunately I seem to be putting more time and effort into building this character in HL, logging bug reports, corresponding with LW and troubleshooting than I am in playing the character. I may just switch back to pen & paper; it may not be as elegant and dynamic as HL, but it's certainly easier to put together.
P.S. For now you can use the adjustment "Natural Attack: Secondary" to force the Bite attack to be a secondary weapon. Just thought of that sense you have the Basic Pack installed.
Yeah, that works to apply a -5 to attacks, but it doesn't change the damage bonus unfortunately; that'd require another adjustment I guess.
Please don't get me wrong; I appreciate your suggestions and the background reasoning you've offered. And I'm not trying to argue the rules with you. I'm just growing disillusioned with a piece of software that's cost me a fair chunk of time and money which I can't yet make use of for this character.