Hi pupoy is 5months old vet has emptied anal glands twice the second time just under a week ago since day 3 he has been scooting again but now really agitated and cheeing at rear end an awful lot i had a look but to be honest he is a hairy black dog so its difficult to see but the bum hole itself looks a little sore/swollen unsure of what glands look like and how close they actually are to the hole itself but he seems to flinch when i. Want to take a look surely he cant need them done again it was literally days after he started this he is fed raw has probiotics poos are normal so why isnt he expressing naturally if that is what is wrong here he is scooting like crazy and gnawing at back end like mad. We have out a e collar on today but feel really sorry for the little guy i am going back to vet hopefully tomorrow but i dont want her to keep fiddling around there i would rather he express naturally i red the more they are done the worse it gets

Not all dogs have perfectly-positioned anal glands to make for easy natural expression. It sounds as if his bottom is still a bit sore from when they were expressed. Sometimes the vet will give a short-acting steroid injection to take away any lingering itch, but a dab of sudocrem can also help.

Yes i put sudocrem on yesterday and today but again this evening he started going crazy spinning trying to bite it again after i was advised by online vet to compress calendula and salt in warm water which has seemed to make things worse

Silly thought, but could he have fleas? River did almost exactly the same thing about 4 days after having his glands done - very agitated, licking and nibbling his bum, getting up suddenly and looking round at his back end, something clearly bothering him back there, very unhappy to be confined because he felt like he needed to move around to “get away” from the sensation.

Vet said his glands were fine, but they spotted a few fleas and he’s probably allergic, they must have been driving him mad. It really did look like his bum was bothering him though.

I usually use Advantage every month in summer and every 2 months in winter, but if Riv’s allergic I’ll have to do it more often.

give your puppy a fast vigorous play in the garden- lots of leaping around and running- it may help shift some of it. also when he comes back indoors will be tired and less energy to pick at himself. 
ps puppies don't care if garden is dark as long as its fun

If the glands are working as they should, and as suggested (and like with my Frankie) they are not too far back for them to be working properly as each normal stool is passed, they should never need draining manually.  And for sure, once messed around with, it can take some time for them to settle down again.  I was able to externally drain most of my hounds glands, if and when needed (which wasn't often) but Frankie's AGs I couldn't and didn't like going in to empty them - because of where they were sited.

Fact is, if these glands do become impacted and infected, they need treating with antibiotics, and worse case - even removed which is a surgery to be avoided if possible as it's not nice.

I'd look into fleas if he's suddenly reacting to something back there.  If at all possible, avoid the need to manually drain the glands - and they will refill in any case as they shouldn't ever be 'empty'.

Am I reading your post correctly? You are using an e-collar to stop him getting at his rear end?

I think the op means an Elizabethan collar aka a buster  not an electric collar.
I've made that mistake before

I don’t think it’s uncommon for small dogs to have incorrectly positioned anal glands that just don’t empty enough no matter how well-formed and solid the poos are.

River’s poos are always excellent but he still needs manually emptying about every 3 months.

I always get the vet/vet nurse to do them for a few reasons - he’s fear reactive to anything uncomfortable or painful, I think the finger-in-bum method is less uncomfortable and that’s not something you should do without training, and also I can’t tell if he just needs emptying or if he’s infected or got an abscess or something which I could make much worse by squeezing.

Sorry yes i meant elizabeth collar not electric no way would i ever use that