What happens after you have completed all agency missions in Just Cause 2

I found the exact same thing. The only thing I could surmise is that it is a way of increasing the difficulty curve.

There is probably some rubbish justification for it along the lines of "the Panauan military is taking measures to stop you from destabilising their country" or some rubbish. Dunno why they wouldn't just put a bullet in your head and go back to dictatoring...

As for the resource constraints, I'm not overly convinced that they affect anything. Having completed the game, nothing really seemed to change much, other than the aforementioned increase in difficulty when getting 100% on settlements.

Once you've generated enough chaos to unlock another "agency", "faction" or "stronghold" mission a new mission icon (grey star for agency, yellow/red/? for factions) should show up the map. You can start the mission by going to that location and activating the mission (usually by pressing the yellow "Y" button at a roadside kiosk looking thing).

The progress bar is used to show how much chaos you need to earn to unlock the next mission, but is only "active" if you've already played through all the open missions in that category.

Your bars aren't active b/c you've already earned enough chaos to unlock a bunch of missions in each category that you haven't played yet (you're map should have a bunch of stars on it). Once you play through all of the unlocked missions in a particular category it should activate again to show you how much more you need to unlock the next mission.