I have this configuration:

Mikrotik 2.9.4x with 3 interfaces
1 - link to the internet
2 - web server + radius server + pc
3 - pppoe clients

It works perfect, till 3 days ago when we change 3 interfaces with 1Gb lan

After few minutes pppoe service crash. In log I see "peer is not responding" and users disconnect.

I change 3 interfaces with 100Mb, and I have still "peer is not responding" for pppoe users. PC's on interface2 (dhcp) is working without problems.

What should I do?

What is your card chipset ??

1Gb cards are SMC (realtek chipset).
1G switch (24x100Mb + 2+1Gb) also SMC

realtek 8169 chip has bad history ROS (check ROS change log)
http://www.mikrotik.com/download/CHANGELOG_rc
http://www.mikrotik.com/download/CHANGELOG_full

so i think you should use any card with Intel chip or the cheep realtek 8139

i am elso experiencing peer is not responding issues. at first i didn't take it into account but now more and more customers are complaining. Mikrotik should do something about this crap or start other business at which they perform better because it is simply outrageous and absurd. I am completely disappointed by the fact that after so many years pppoe implementation is still partially broken.
My setup is RB450G with 60 connected clients 20->60 Mbps down, 10->20 Mbps up, but traffic doesn't really matter as far as i see. It occurs at 10 Mbps and also at 60 Mbps at the same rate. While running RP-PPPoE on Ubuntu Linux i did not ran into this problem, and now i will go back to that setup.