Removed one of the hopper patches in 1.8.3 which I think caused this. Hopefully its fixed
weird did you need to replace the hoppers once you patched it or did they auto fix? my sorter and auto-smelter are still only half working
These options fixed it for me :
hopper-alt-ticking: true
ticks-per:
hopper-transfer: 7
hopper-check: 7
hopper-amount: 1
But I have still the issue that hopper clocks (2 hoppers facing each other) stop ticking when unloading then reloading the chunk.
Thank you but that did not seem to help either still broken using this:
hopper-alt-ticking: true
ticks-per:
hopper-transfer: 7
hopper-check: 7
hopper-amount: 1
that did not solve my problem. it keeps getting MEGA HIGH SPEED after a chunck reload or server restart
https://hub.spigotmc.org/jira/browse/SPIGOT-333?focusedCommentId=11424&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11424 has a solution to this issue.
Hope this gets resolved, everything that relies on hoppers does not work. Only way to get a broken hopper to work is keep breaking it and placing it back until it works. But if you leave the chunk or server restarts it randomly breaks/fixes hoppers.
This Bug also occurs when Worldguard regions overlap. Where they overlap, the hoppers disapear.
It would be nice if this bug didn't occur when hopper-alt-ticking is set to false too.
Had this problem over on Merecraft using git-Spigot-13716d9-0899683. Solution was to enable hopper alt-ticking. Somewhat annoying, but in the end it's a more performant solution anyway.
This also makes item sorter buggy. instead of pulsating when filtering, the hopper which is connected to the comparator outputs sometimes a pulsating signal, sometimes a constant signal and sometimes no signal at all when it doesn't even pull the items for filtering. Anyway Redstone has always been rather buggy under spigot.
Confirmed as of build git-Spigot-52c130f-81ab957
It happens randomly on hopper clocks.
To fix it you have to break and rebuild the clock manually multiple times until it's ticking normally.
Sometimes it bugs even more, one of the two hoppers outputs a constant redstone signal and the other one doesn't output anything with a comparator.
Video showing the bug.
On the left, the normal ticking rate, on the right the buggy ticking rate.
http://youtu.be/ILbgTFbLpLk
Mainly seems to affect hoppers with 1-2 items in them, while hoppers with 3+ items SEEM to tick normally - for example clocks with two Hoppers facing each other, A gives it to B, and B seems to give it back to A one tick later - not sure though if it's one Gametick or one Redstonetick (2 Gameticks), but I think, it's at most one Gametick, due to Comparators not reading the item inside Hopper B at all.
Even though this isn't really a fix, but after playing around with the settings hopper-transfer and hopper-check in spigot.yml - I may just have been lucky, but the issue almost (though not entirely) vanished for existing hoppers when I changed the settings to:
hopper-transfer: 6
hopper-check: 10
I just noticed on a testserver (pre-1.8 testworld) that with transfer being lower than check, the issue seems to be less frequent. 6 and 10 should have been almost identical to the default values in terms of noticeability, but when implementing this change to our liveserver, one of our players noticed some of his hoppers to transfer items too quickly, compared to 1.7 - so I increased the two values. Everything from 7/11 to 9/13 made it worse, and on 10/14 it suddenly got a lot better - most devices using hoppers suddenly worked, even though hoppers were slower due to those settings.
But as I said, we may just have been lucky there - changing values around so much might have been the actual solution. Are information like "update this and this block at tick now+x" stored when a server shuts down? I also played around with clear-tick-list and hopper-alt-ticking (the latter of which only worked the first time; after that, it made hoppers not do anything at all anymore), so this partial workaround might not actually be helpful. I just thought I'd share those information anyway.
This could also be relavant: http://www.spigotmc.org/threads/hopper-chunk-bug.38960/
Certainly a Hopper issue on my server as well since update. I can go back to 1.7 and not see same issues.
with me it happens all over the world 
i have to replace some hoppers every restart to make them work normally
Haven't noticed it myself. Perhaps someone could upload an affected map/chunk? (with coordinates of where it is)
Confirmed on the Craftbukkit version of 1.8 also
Still occuring in git-Spigot-612de46-07c2162 (MC: 1.8) (Implementing API version 1.8-R0.1-SNAPSHOT) This bug breaks hoppers as item at certain areas, this should be rated as important
Noticed fast hopper tick in my server too, in certain areas they instabreak if you put an item inside
it also happens on worlds from earlyer spigot versions that now run on 1.8 spigot