Very possible this is related to a CIA operation
designed to undermine the government of Ecuador.

Also possible that it was done to punish a competitor of a group that CIA finds easier to do business with.

My [[guess]] is they took down the people that built the thing or the crew on cargo for the boat, or they were trying to do that and the perps ran off, and so they were left with a boat they had to go ahead and seize or everyone would question why they hadn't seized it.  People like "yestotruth" for example.

And yes other similar boats have been seized including some at sea that were not able to be scuttled in time by the crew, though I suspect that maybe they really didn't want to scuttle the boat and then not be picked up.

One thing though, this boat was larger than some of the others I have seen remarked on.

Ok, I found this:

"Since 2006, when the first semi-submersible craft was detected, 47 have been captured at sea and on land - including 17 last year. But so far this year, only three have been captured. The number of voyages has probably dropped, officials said, because of their success in detecting the vessels with a variety of methods including aircraft that can identify their wake in the water."

at:

http://www.sacbee.com/2010/07/05/2870344/authorities-seize-100-foot-narco.html

This one is actually a much more advanced sub than the others.

By the way, I have a friend who commanded a real USS submarine.  One night they were under way down in that same area and were cruising on the surface and though the main bulk of the ship was under water, the tower is pretty high. Anyway, at first they noted that there was someone else in the area at a good distance, and then that the other ship was making considerable knots to catch up to them.

The sub did have running lights and such, but obviously the other ship a coast guard vessel didn't recognize what they were coming up on from behind, and suddenly the sub and my friend, commanding, were hailed with the cutter identifying itself and essentially ordering the vessel with those lights over there to identify itself and to "heave to"

My friend replied some what caustically that "This is the ** nuclear ** USS **" and "How are you doing this fine evening?"

We assumed that there were some red faces over on the cutter, and then some fond farewells as both vessels went their separate ways with a new sea tale to tell when the lights are low.