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We are looking for a game that can be played skirmishes or 40k style and still have D&D playable situations. Is their a game out in the wild that does this?

You're not going to find one ruleset that does all those things (Large Battle, Warband skirmish and RPG) well. Games are written for one scope for a reason. Different size games require different kinds of mechanics and anyone who says their game "scales from skirmish to mass battles" should be viewed with suspicion.

However, there are some possibilities to get around this.

Battletech has separate rulesets for different scopes. Each of these rulesets has the ability to convert experience, money, forces, etc into other systems for use in a campaign. They Have:
-RPG: Time of War
-Platoon of Men: Battletroops
-Squad of Mechs: Battletech
-Platoon to Company Level: Alpha Strike (my favorite of the batch)
-Battallion Level: BattleForce
-Space Combat: Battlespace

Consider companies that have similar -though not deliberately compatible- ranges of products. It's not hard to develop your own way of making one game link to the other.

The 40k universe has:
-40k
-Inquisimunda -A great fan adaptation of Necromunda into the larger 40k universe
-Inquisitor (RPG-ish miniature game) Many folks play it in 28mm, look for "INQ28"
-Dark Heresy/Rogue Trader RPG
-Epic 40k Harder to find figs for, but their are proxy options.
-Apocalypse. I'm hesitant to offer it since it's such a total cop-out. Instead of actually being a ruleset with the necessary streamlining for battalion level play, they add more complexity and expect you to take and entire day to play it.

Privateer press has both Warmachine and the Iron Kingdoms RPG

Or if you folks want to do the DIY Fantasy or sci-fi thing, grab rulesets from a variety of sources that fit the scope of game you want and work them into your own universe. Our club does this with our "Galactic Frontier" setting.
http://chicagoskirmish.blogspot.com/p/galactic-frontier-homebrew-sci-fi.html
We've got:
-Space Battles (Full Thrust)
-Mech Combat (Mech Attack)
-Platoon skirmish (Tomorrow's War)
-Warband Skirmish (In The Emperor's Name, The Dogs and The Dust)
-Post-Apoc-style combat on ruined worlds (Nuclear Renaissance)

Admittedly, it's not organized into a cohesive campaign, but it's nice to have a setting into which to place your battles.

I'd add the old FASA Renegade Legion games to the list

There is an RPG Renegade Legion: Legionaire

then you've got

Renegade Legion: Interceptor for dogfighting style space combat (I still love this)

Renegade Legion: Centurion for armoured combat (great fun, but probably feels a bit dated now)

Renegade Legion: Leviathan for space fleet engagements

and the one I never had

Prefect which was I think a map based high scale boardgame with lots and lots of counters

(oh and an SF chariot racing game in the same world setting which is loads of silly fun)

Thanks for the comments I will probably use a few games to make our own Setting playable.

Striker.

In the rules it pretty much explains that you are NOT "playing" the platoon, company, or battalion.

RATHER... You are playing the CO of your platoon, company, or battalion.

You issue orders, or directly lead men to control the "miniatures" representing them.

The game pretty much requires a GM.

MB