My mare got blood clots in her jugular vein in December of 2007. We took her to the vet, it got better, but then she got another one in her other vein (where the IV was). Once that went away, we didn't have another incident until a few weeks ago. She now has them again in both jugular veins. She actually has two separate ones in one vein, and another in the other vein.
I plan on asking my vet about it, but I wanted to hear from other people too. I'm surprised he hasn't mentioned something about it.