Vlan/trunking issue, converting inherited flat network to router on stick vlan

The cisco router had a bunch of secondary ip's on its lan interface. So after upgrading the switches throughout I started migrating the secondary ip's to sub interfaces. My understanding was sub interfaces should work even if the main interface has ips on it. But, while I can ping other vlan ip's on the router from the native vlan (1), I can't ping the non native vlan ip's on the router from their own vlans. So switch1 port 10 has a client with ip of 10.0.2.5 say, and it can't ping 10.0.2.1. But it can ping another client, say 10.0.2.6 on switch2 port 10 no problem. I have no idea why. I thought maybe I was wrong and subinterfaces don't work when there are ip's on the parent interface, but then I can ping 10.0.2.1 from other ports not configured for vlan 20. What gives?

Router: Gig0/1 ip address 10.0.0.1 255.255.255.0 ip address 10.0.1.1 255.255.255.0 secondary ip address 10.0.2.1 255.255.255.0 secondary to: gig0/1 ip address 10.0.0.1 255.255.255.0 ip address 10.0.1.1 255.255.255.0 secondary gig0/1.20 encapsulation dot1q 20 ip address 10.0.2.1 255.255.255.0 switch1 gig1/0/10 switchport mode access switchport access vlan 20 gig1/0/48 descrition uplink to router switchport mode trunk gig1/0/49 description uplink to switch2 switchport mode trunk int vlan1 ip address 10.0.0.2 255.255.255.0 switch2 gig1/0/10 switchport mode access switchport access vlan 20 gig1/0/49 description uplink to switch1 switchport mode trunk int vlan1 ip address 10.0.0.3 255.255.255.0