Can you run both EoIP tunnels via the same L2TP connection and distinguish them from one another using tunnel-id, or you have some reasons to use two independent L2TP connections with independent user names? I’m afraid that two L2TP clients connecting to the same server are causing the trouble, as they use the same UDP port at both local and remote end.
It’s really weird. I’m using multiple EoIP tunnels differentiated by tunnel-id and there is no problem. But there may be some interaction with the firewall - EoIP misuses some header fields of GRE for the ID which may explain the difficulties of connection tracking with GRE packets carrying the EoIP payload.
Please follow the hint in my automatic signature below for both the L2TP server and the L2TP client, I’ll suggest you some firewall rules to add which may help. In short, GRE handling has been “improved” a few RouterOS versions ago, and since then you have to add rules to let incoming GRE packets get through.
Also, if you don’t need to use VLANs on the L2 tunnels with vlan-filtering set to yes on the bridge, you may avoid the issues with GRE handling and save some packet space by using BCP, which creates an L2 tunnel in parallel to the L3 one using L2TP alone.