Do you have a VLAN interface underneath the pppoe-out interface? Maybe you can temporarily turn on logging for PPPoE by adding a new rule for that topic under System → Logging:

You should see in the log that, when initiating the PPPoE connection, your router broadcasts PADI messages, with ppp-max-payload=xxxx (1492 if you didn’t set Max MTU and Max MRU, otherwise their value will be here).
The other side will send back a PADO message. Does it message also include a ppp-max-payload parameter (it would if the PPPoE server supports RFC 4638)? If yes, is the number smaller than 1492?
After that your router will send out PADR message, and get back PADS message. Then there will be several LCP messages being sent back and forth. Do they specify the mru value (such as 1492)? With the LCP messages, the two sides will also agree on the MRU value (MRU of the other side is MTU for your side). Is the agreed MRU value still 1492 or has it been lowered after the LCP exchanges?
Then authentication will be performed. Once this is done, your router will do something that I think is relevant to your issue: It will try to send a LCP echo message with a very large payload, the payload will be chosen so that the packet reaches the MTU/MRU agreed above (in this example below 1484 + 8 = 1492):

If the PPPoE server sends back a EchoRep reply with the same payload length, then the MTU/MRU value is valid and will be displayed in Actual MTU in WinBox. If, however, the underlying ethernet layer could not send a packet that big, no EchoRep will arrive. After a timeout RouterOS will reduce the MTU/MRU of the connection to 1480.
Because my ISP supports RFC 4638, I can replicated this issue by making a PPPoE connection with Max MTU and Max MRU set to something that will later cause the EchoReq message to be larger than my L2MTU. My L2MTU is 1510 and I’ll try to create a PPPoE connection with Max MTU = Max MRU = 1506:

Red arrow is my router setting ppp-max-payload in PADI and blue arrow is my ISP saying that that’s ok because it supports RFC 4638. Next is the agreement on MRU and PAP as authentication method:

Authentication succeeded, and here you can see my router sending out the EchoReq message to test whether a packet with size 1506 could really be sent (1498 + 8 = 1506).

This packet will require the ethernet layer to be able to send 1514 bytes payload (1506 + 8 = 1514), but my L2MTU is only 1510:

So it could not be sent, and no reply will be received. After a few more tries RouterOS will drop the Actual MTU to 1480!

I suspect this is what happened with your configuration, it also explains the 5-second delay before the MTU drop (it’s the wait for the EchoReq tries). And I have seen others observing the same problem, and one thing they have in common with you is that they were also running RouterOS on x86.
I suspect that your network adapter has a low upper limit for the max possible MTU (what MikroTik normally shows with L2MTU). Maybe the adapter supports ethernet frame just large enough for the usual ethernet header and trailer for a 1500-byte IP packet. That’s why I asked above if you have VLAN set up. Normally with VLAN the ethernet frame must be able to grow by 4 more bytes, if you still want to be able to send an IP packet of 1500 bytes. MikroTik hardwares all have L2MTU > 1500 + 4 so you can always enable VLAN and have no problem with MTU 1500. But that’s not necessarily true of the network adapter in your x86 build. Does the adapter have a setting toggle for VLAN support?