Why can't I raise levies from half of my counties?

I took a break from playing Crusader Kings II for a few months. Since I've come back (November 2012), I'm suddenly unable to raise levies from most of my counties. The button is grayed out, even though there are some levies available to raise in the county. (The green/red bar for the levy in the county info screen is mostly green.) The most distressing part is that some of those counties could raise ships, and so now I have more troops than transport.

I tried raising all available troops from the Military screen, but most counties don't have any army on them. How did raising levies change?

Patch 1.07 changed the way that levies work. From the patch notes:

• Liege levies. You only raise levies from your direct vassals, and they are not directly connected to Holdings.

More detail from this CKII development diary:

In patch v1.07, you raise fewer, larger levies from your direct vassals (we call these "Liege Levies" for lack of a better term.) These levies are now handled separately from actual Holding levies; you only get regular holding levies from your own Demesne. The opinions of vassals of vassals are thus now mostly irrelevant; you only need to worry about the opinions of your direct vassals. Another benefit is that you don't get tiny little armies all over the place when you mobilize your realm. Liege levies also fix a fundamental balancing flaw in that you can no longer just keep raising little levies from all vassals as a war drags on (due to the portion of holding levies that was reserved for the liege.) The new Liege Levies do not reinforce at home while raised.

in one of the latest updates (patch 1.07) they made it so instead of a whole lot of mini-levies, now you get one big levy per direct vassal. You only get regular holding levies from your own demesne possessions.