We have over forty usergroups, all which we consider vital and over twenty-five thousand members. On larger forums we're noticing a ton of time outs, primarily, Server Did Not Respond In Time. We tried the fixes here. But, they do seem to save but, we still get the error spat out. Our statistics:
Total of 41 usergroups.
We consider most vital, and, we haven't had this problem of a slow admin panel on our old software. We're pleased that posting/thread making is fast/normal and responses are. It's just it's quite slow creating new nodes, using an addon permission like LiquidPro's Simpleforms that has to update all usergroup permissions, or saving new permissions for a usergroup that's large.
Lots of groups + lots of nodes = slow save time when editing groups and nodes. XenForo does extra processing at save time to maximize performance at run time. My post that you linked to is the solution:
No error is being produced besides server took too long to reply. :/ We already tried those fixes. Not working. Most of the time the change/edit do save, but, there are sometimes they don't and they always come back saying server error log