I don’t know if this helps much, but the authentication issue has been a problem since forever on 2.9.x (not 2.8.x, 2.8.x was slow but solid)
It just turned much worse after 2.9.25 when they changed the way they synchronize the login procedures.
http://forum.mikrotik.com/t/heavy-loaded-pppoe-server-troubles/13065/1
The problem, as i see it, is race conditions during login setup that happen under high cpu load (which btw, authentication is apparently quite the cpu hog in routeros). I know how to minimize it but not know how to completely remove it.
support@ proclaimed that / ppp secret lists was not designed to handle this, but I’ve seen the effects when using RADIUS as well.
Anything that slows the login procedure will only make it worse.
I have no trouble having 700 - 800 users login at the same time ( on 2.9.24 ) but every 3-5 months, when the server has had time to leak enough memory and thus slow things down, a single user can destabilize the whole server. I’m sure if we replaced the cpu with something faster than the 2ghz Xeon (P4) with 512 KB cache, we wouldn’t see it that often but we have adopted a different strategy all together.