I've got two slightly different bolt carriers in two uppers, both from JT (one varmint upper bought new, one 16" A3 from the EE), and one's hanging up while I'm function testing a trigger in the lower.  

Can someone tell me why they're different and if it will affect how they work?  The one with the cutout is hanging up as it goes forward with the trigger held back.

http://www.maxicon.com/guns/ar15_bolts.jpg

The area around the firing pin on the top carrier is the type designed for an M16 carrier. The lower carrier is what is known as an SP1 style carrier. The SP1 carrrier was made to be used with an SP1 type firing pin and an SP1 Type hammer. One purpose of the SP1 designed parts is to catch the carrier and stop its forward travel if the hammer was not retained by either the disconnector or the trigger during the normal firing cycle. It acheives this by a notch in the top of the hammer catching the large exposed collar at the rear of the firing pin. Problems happen sometimes when the wrong type firing pin or hammer are used with the SP1 designed carrier or when the parts are out of specification. It is not uncommon for an SP1 firing pin collar to be wider than it needed to be and cause the hammer to catch on the too large collar. Also using an AR hammer without the notch can cause problems. The notch lowers the height of the hammer when it is cocked which keeps it from hitting the pins collar. Some of the notched hammers I have were notched incorrectly. This can caused them to hang also.

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Thanks for the detailed info.

If I want to use both uppers on the same lower, it sounds like I need a new carrier to match the hammer in the lower for one of the bolts, and need to check the FP as well in case it needs to match.

My hammer came with the upper bolt, so I'm assuming it matches that, but I have to check.  Is there somewhere with pics of the two types of hammer that make it easy to compare?

www.biggerhammer.net/ar15/hammers/
The top two on the right are the common two. The far top right one is the SP1 style.