My puppy was on i/d long term because of loose/runny stools - and he's still alive fit and well. He didn't have a choice though. Prescription i/d is the absolute best food for upset bellies!
My pup's issues sound similar to yours he also had fecal floats, checked for worms etc.
He had parvo when he was little so that may have had something to do with it, or maybe I was overfeeding when I was trying frantically to put weight back on him post parvo. I was given i/d after parvo to feed during recovery and kept him on it for about 6 months it was the only thing I knew he could eat without issues. I now keep cans in stock just in case we have any problems.
We also ditched the kibble completely, I reduced the amount of food I was feeding and I now make and blend a 'vege mix' from scratch and add to fresh raw pet chicken mince. We haven't had a problem since
What are you doing when puppy gets sick? Are you fasting etc? Sometimes not resting and recovering the digestive system properly may have an impact on the longevity of the problem (or it did when I rushed and fed my boy too quickly anyway...). Also speak to your vet about getting Protexin or similar to restore good bacteria in the gut.
My routine for runny stool is fast the minute I see any problem for 24 hours (depending on age less if puppy check fasting period with your vet), I make him a soup with a chicken frame (just to add flavor) that I feed to keep hydrated (skim all fat off, fat is not your friend when you have puppy with diarrhea). I usually feed the soup in the last 8 hours and mix some Protexin (puppy probiotics) in it - (someone here suggested I get some from the vet and I haven't looked back). Introduce the i/d slowly small meals frequently and add Protexin in for a few days then he would go back to mr ball of health.
I haven't had to do this though since he changed diet (touch wood anyway).
Good luck with your pup I hope it's something simple to fix.