I have been experiencing the same issue.
I use routing mark, but only for some specific traffic (pppoe related).
I have 2 subnets configured on the CRS125, but on the same port, port-13, and port-13 is the master port for ports-14..24. Lets say i have
192.168.1.0/24 on ether13 (router address is 192.168.1.1)
192.168.2.0/24 on ether13 (router address is 192.168.2.1)
And in the other hand, I have a separated subnet configures on wlan1
10.254.0.0/24 on wlan1 (router address is 10.254.0.1)
on my routing list, I have the 2 dynamic routes related to both subnets on ether13 and another for wlan1.
When I connect to wlan1 with a notebook for example, I can ping the CRS (on IP 10.0.0.1), I can ping 192.168.1.1 and 192.168.2.1, except I can't ping remote devices on any subnet.
Sometimes I can ping devices on one of those subnets, for example, I can ping a computer with address 192.168.1.10 connected on any port from ether13..ether24, but not any remote address from the subnet 192.168.2.0/24.
The only difference I could see between those subnets is that on the route list, I have some pppoe dynamic routes that goes in the middle of the routes, like this.
# DST-ADDRESS PREF-SRC GATEWAY DISTANCE
0 A S 0.0.0.0/0 y.y.y.y 1
4 DC 10.254.0.0/24 10.254.0.1 wlan1 255
5 ADC 192.168.1.0/24 192.168.1.1 ether13 0 <--- I can reach remote addres on this subnet
6 ADC x.x.x.x/32 10.x.x.x <pppoe-xxxxxxxxxxx 0
7 ADC x.x.x.x/32 10.x.x.x <pppoe-xxxxxxxxxxx 0
8 ADC x.x.x.x/32 10.x.x.x <pppoe-xxxxxxxxxxx 0
19 ADC 192.168.2.0/24 192.168.2.1 ether13 0 <-- but not on this
I think that, in my case, the dyanamic routes related to pppoe clientes are somehow getting in the way of my ability to reach 192.168.2.0/24 subnet, and since I can't confifure the order of the route list, I can't see a way to test that theory.
I'll be following this thread, and if I found out anything new, i'll post back here also.