I would tend to believe they came in with them. Where did you purchase them? It's really good that you can catch this while they are still eating.
I found a posting on simplydiscus.com where two people successfully used the exact same dosing method of Seachem metronidazole available at
www.jehmco.com to treat intestinal flagellates: And by the way, notice he mentions the type of frozen bloodworms...ever since I began keeping discus I have seen where many people say that Hikari frozen bloodworms are the best to use for discus. I've read many posts where fish became sick while eating other brands. Hikari is known for their special sterilization methods to ensure pure product. Hope this info helps, flagellates in discus are a battle!
"what i did was to put around 5 to six measures(it should have a small spoon. i made sure that when i pick the powder with the spoon i wouldnt make a hill so there would only be powder to the height of the dept of the spoon like dont over fill the spoon) for 40 gallons raise the temp to 90 to 91 F let the med stay for 38 to 48 hours meaning that when you feed (if they are eating)
and you syphon the left overs dont add any fresh new water to the tank. the original water should stay with the med for 38 to 48 hours.
then do a 95% water change. now when you want to add med again you can just pour the same amount in the tank and start filling it but what i did which might not be recomended by many hobbyists was to pour the med right in front of the fish when there is only 5 to 10% water left when i do this because the fish is breathing, while breathing some med particles will be swallowed by the fish. of course most of it would be spit out though. and then i would start adding fresh water. it took me 6 treatments that is 12 days to treat the fish. they start eating on the 3rd or a day before the 4th treatment. after 12 days i kept the water at 91 F for another 2 weeks so the fish would eat 5 to 7 times a day to get health back also in this 2 weeks i started adding top fin conditioning salt found in pets mart.
i add almost one measure for evey 5 gallons (i added salt to keep stress away). also in this two weeks after syphoning the leftovers i add fresh water to the tank. then at night right before sleep (2:00 AM) i change 90 % of the water.
do not put 2 measures of this med for every 10 gallon it will overdose making the fish dark and if kept in the water without WC. your fish may bleach out starting to swim like it has gone blind. if this happened do 140% WC every day for 3 days with no meds at all.
after the fish get completly healthy i recomend water change more often also be carefull what brand of blood worms you feed. i noticed when i use San Francisco Bay blood worms my fish get sick i stop using it and switched to hikari Because it looks more fresh, brighter red compared to the San Francisco Bay one."