Hi Peter, and welcome! I'd suspect intestinal parasites ("worms") if they're eating well and the feed is decent quality. There are commercial anthelmintic drenches and I hate to use them or advise others to go down that path, because they mess up the animal's gut biome and, worst of all, they never eliminate all the worms and the ones that survive pass on their genes. Voila: drench-resistant parasites. It's become an arms race here, especially with sheep.
We had alpacas for 18 years and had very minor worm burdens. The best thing you can do is prevent them from building up by rotating the animals and resting paddocks longer between grazing. Most stock parasites need live hosts within a certain time frame to maintain their reproductive cycle, and if they wait too long they die out because they can't travel very far on their own.
Feeding hay can help, with the extra roughage pushing things along. Feeding tree branches like willow is very beneficial because of the condensed tannins, which the worms don't like. Some legumes have lots of condensed tannins too. Biochar is pretty amazing for controlling parasites...we have seen egg counts drop to zero in weaner cattle that were eating it daily. You can get an alpaca to eat biochar by mixing it with some molasses, lucerne chaff, and salt. This is also a blend that works for sheep. Cattle will eat it straight.