Im so sorry to hear about your boys. Im recovering from 5 months of C Diff as well, and know as fact that the stool cultures for C Diff can be innacurate. Ive tested "false negative" many times, as the antibiotics seem to mask the results. From what Ive studied, its best to do the assay test 10-14 days from the last dose of Flagyl/Vanco - two days of sample in a row. Also (again, this is just what Ive learned by battling this nasty bug for months), one can still test "postive" for the spores, yet not be ill if the spore isnt producing the toxins A/B. Each doc Ive spoken to has had a different treatment protocol, but statistically most seem to recover with 1-2 rounds of antibiotics. Flagyl failure rates are rising as well, and a Vanco round followed by a Vanco "taper" is when I seemed to have turned the corner with this thing. Probiotics advice is also a great question to discuss with your Pediatrician, as Ive also used them throughout my treatment. There is a wonderful website, cdiffsupport.com that compiles the most recent studies, along with a great discussion board - alot of good information on C Diff and children as well. All my best to you, and I hope your boys feel better soon.
I am definitely no expert on infants, but I know a little about indigestion. First, I think your report that their stools are better, this is a good sign, I hope it stays that way. The smell and everything else was likely from stool getting backed up and rotting in the digestive tract, because antibiotics are notorious for clogging up the system. I think the vaccocin was the better medicine than the flagyl. I think the flagyl worked a little, but not enuff; likewise the vaccocin worked harder, and finally got it right. I also would be wary of a scope, too.
One thing you can ask your pediatrician is if giving them Acidophilus milk would be okay. Just a couple cups a day, for two or three days, will restore the "good" bacteria in their system. Anytime a person takes an antibiotic, it kills "all" the bacteria, good and bad, so sometimes it helps to give the digestion a boost by restoring the "good" bacteria with the probiotics that are in Acidophilus products. I have read articles that theorize the reason children get repeat ear infections is because of that effect, antibiotics killing all bacteria, so they are left with no bacteria to fight infection. Probiotics, which are in Acidophilus milk, restore the bacteria needed to fight infection. Just my ideas.