I have two buildings set up using two Mikrotik routers and IPSEC. Router one 192.168.1.1 Router two 192.168.5.1.
The tunnel is working great and all access from one location to the other works great.
The problem I have is when I attempt to RDP or VNC. If I VPN into router one 192.168.1.1 and try to RDP to that subnet 192.168.1.0/24 I can't. I can RDP to the other subnet at the other end of the tunnel 192.168.5.0/24.
If I VPN into router 2 192.168.5.1 I get just the opposite, I can't RDP to 192.168.5.0/24 but I can RDP to 192.168.1.0/24

Not sure if it matters but
My firewall nat is setup with:

Router One
Chain: srcnat
Src. Address: 192.168.1.0/24
Dst.Address: 192.168.0.0/16

Router Two
Chain: srcnat
Src. Address: 192.168.5.0/24
Dst.Address: 192.168.0.0/16

For anyone that is having the same problem I found the solution.

The problem or solution was in the interface.
For each interface that is connected to the local subnet simply change the ARP on the general tab to proxy-arp and that will solve the RPD over IPSEC issue.

For those that have a bridge setup you can also just change it there and any interface associated with that bridge will also be affected.