These hindrances and skill adaptations are meant for a game where pc vs. pc conflict is good, even desirable. Players should understand that they should play their characters with feel rather than optimal efficiency - and if they do should be rewarded with bennies. These flaws can get pc's in quite much trouble, so an additional benny use for creating small story twists works well with them.
Knowledge (Military) and (Law) aren't new skills - they are commonly used in various settings, but these rules give new uses for those skills.
Some of these flaws and rules have been inspired by Battlestar Galactica series and Roleplaying game; white I didn't like Cortex RPG as a roleplaying system after all, BSG:RPG is a cool book and the rule system had several good things too. BSG:series did excellent job with tensions between characters and their flaws.
Conflicting loyalties (Minor/Major)
You are secretly in service of someone. This someone might have goals conflicting those with your allies; you are occassionally contacted by your employer and assigned tasks. You may also have initial ongoing task(s); GM may assign them to you or you may suggest tasks of your own to your GM.
If your mission may involve actively manipulating or sabotaging your group's mission, or your mission causes frequent or major drawbacks to your group as a side-effect, this hindrance is Major.
Bad temper (Major)
You get easily pissed off. You start picking fight for slightest reason, for example if someone says something you don't like or you just have a bad day. If you have a bad day and someone says something you don't like, you might well respond with a fist, ignoring consequences.
You have some self control though - you don't smash a foreign ambassador's face for example - unless he REALLY annoys you; you might make some nasty remarks though. On societies with weaker laws and morale, you might also turn to lethal violence against those that piss you off.
Blind obedience (Major)
You are part of a military or paramilitary -organization, and have learned to obey orders without questioning them. When receiving conflicting orders, you need to obey the highest authority. Your own commander is considered to be one rank more influential when competing against a commander of different unit, and own commander wins any ties. If you are following orders of a higher rank commander and get new conflicting orders from a lower rank commander, you need to get confirmation for this change of orders from higher level or refuse to follow. (You can find rank information under Knowledge (Military) skill)
It is possible to make you believe that a higher authority has gone fugitive. This requires acceptance of other soldiers, some evidence and persuasion check at -2 or more (no modifier if there's very strong evidence). Even higher authority, or very strong proof AND some great persuasion is required to convince the soldier that the target isn't fugitive.
It is possible to persuade a character with Blind Obedience to do something that breaks his orders, but it requires some cleverness; No normal persuasion works without some believable reason why the character isn't ignoring his orders ("You can't guard the treasure by standing there, as it has been stolen by digging through the wall! It's being carried to the harbor at this very moment!").
You don't like authorities. You can't keep your mouth shut near them, 'misunderstand' orders purposefully and are not above punching your superior officer or law enforcement personnel if they get personal. This may get you into loads of trouble and gives -4 reaction penalty from superior officers, law enforcement personnel or other figures of authority, and tends to get you in the worst jobs, thrown in the brig for smallest reason or beaten up by bad-tempered cops.
Obsessive leader (Minor/Major)
You want to be in control. You usually don't trust others to make right decisions and want to make them yourself, and if there's any chance for becoming leader in the group you are in, you will try to claim leadership.
In case of Major hindrance, you are willing to take risks or harm others to claim leadership.
You think of yourself and only yourself. Others are expendable, if it can help you in any way. Troopers are left behind to buy you time, and your friends work well as zombie baits.
You have -4 Charisma towards people who know your true nature.
Skill: Knowledge (Military)
In addition to knowledge about military units and equipment, you know regulations thoroughly – enough to find loopholes and justifications to refuse from obeying orders legally, at least until confirmation is received.
In a conflicting situation, two military personnel may try to make soldiers to follow conflicting orders, making this check contested. Both personnel may add their charisma modifier to the check.
Rank difference: If you are lower rank than the officer giving you an order or who's command you are challenging, you gain penalty to the check equal to amount of rank difference. Trying to convince soldiers of another unit vs. their own officer gives an additional -1 modifier.
Complexity or nature: Complexity or nature of the situation may give modifiers to the checks.
Generic army ranks: General(8), Brigadier(7),Colonel(6), Major(5), Captain(4), Lieutenant(3), 2nd lieutenant(2), Sergeant(1), Corporal(0)
Generic navy ranks: Admiral(8), Vice admiral(7), Captain(6), Commander(5), Ltn. Commander(4), Lieutenant(3), Ensign(2), Petty officer(1), Corporal(0)
Skill: Knowledge (Law)
As Knowledge (Military), but affects civilian organizations and law in general. This may be used to force police to release an arrested person, discard charges or do similar things.