We've been able to reproduce this internally as well, without even rebooting.  I'll add the info here since the multiple active routers seems to be issue, not necessarily the reboot.

$ neutron router-create --tenant-id 8beb0d59ef0a448d9e0da918931f3c22 --distributed True --ha True r1
Created a new router:
+-------------------------+--------------------------------------+
| Field                   | Value                                |
+-------------------------+--------------------------------------+
| admin_state_up          | True                                 |
| availability_zone_hints |                                      |
| availability_zones      |                                      |
| description             |                                      |
| distributed             | True                                 |
| external_gateway_info   |                                      |
| ha                      | True                                 |
| id                      | cb484e8c-4de6-4a50-89d6-e8c53e6f6d4b |
| name                    | r1                                   |
| routes                  |                                      |
| status                  | ACTIVE                               |
| tenant_id               | 8beb0d59ef0a448d9e0da918931f3c22     |
+-------------------------+--------------------------------------+

$ neutron router-gateway-set cb484e8c-4de6-4a50-89d6-e8c53e6f6d4b 72e69016-085b-40a5-94aa-bdacafd5a075
Set gateway for router cb484e8c-4de6-4a50-89d6-e8c53e6f6d4b

$ neutron net-create n1
Created a new network:
+-------------------------+--------------------------------------+
| Field                   | Value                                |
+-------------------------+--------------------------------------+
| admin_state_up          | True                                 |
| availability_zone_hints |                                      |
| availability_zones      |                                      |
| created_at              | 2016-06-15T12:28:46                  |
| description             |                                      |
| id                      | 5b644fea-50b7-49b3-b4b3-88a05509f9a0 |
| ipv4_address_scope      |                                      |
| ipv6_address_scope      |                                      |
| mtu                     | 1450                                 |
| name                    | n1                                   |
| router:external         | False                                |
| shared                  | False                                |
| status                  | ACTIVE                               |
| subnets                 |                                      |
| tags                    |                                      |
| tenant_id               | 8beb0d59ef0a448d9e0da918931f3c22     |
| updated_at              | 2016-06-15T12:28:46                  |
+-------------------------+--------------------------------------+

$ neutron subnet-create n1 99.99.99.0/24
Created a new subnet:
+-------------------+------------------------------------------------+
| Field             | Value                                          |
+-------------------+------------------------------------------------+
| allocation_pools  | {"start": "99.99.99.2", "end": "99.99.99.254"} |
| cidr              | 99.99.99.0/24                                  |
| created_at        | 2016-06-15T12:29:01                            |
| description       |                                                |
| dns_nameservers   |                                                |
| enable_dhcp       | True                                           |
| gateway_ip        | 99.99.99.1                                     |
| host_routes       |                                                |
| id                | b7f2e674-887d-4282-b671-6e8edb5f9524           |
| ip_version        | 4                                              |
| ipv6_address_mode |                                                |
| ipv6_ra_mode      |                                                |
| name              |                                                |
| network_id        | 5b644fea-50b7-49b3-b4b3-88a05509f9a0           |
| subnetpool_id     |                                                |
| tenant_id         | 8beb0d59ef0a448d9e0da918931f3c22               |
| updated_at        | 2016-06-15T12:29:01                            |
+-------------------+------------------------------------------------+

$ neutron router-interface-add cb484e8c-4de6-4a50-89d6-e8c53e6f6d4b b7f2e674-887d-4282-b671-6e8edb5f9524
Added interface 1b410fb9-6e87-49d3-a79d-f8226dd83325 to router cb484e8c-4de6-4a50-89d6-e8c53e6f6d4b.

$ neutron l3-agent-list-hosting-router cb484e8c-4de6-4a50-89d6-e8c53e6f6d4b
+--------------------------------------+-----------------------+----------------+-------+----------+
| id                                   | host                  | admin_state_up | alive | ha_state |
+--------------------------------------+-----------------------+----------------+-------+----------+
| 3807a338-66c1-4812-afe8-30486ce7b593 | hlm004-cp1-c1-m1-mgmt | True           | :-)   | active   |
| 7e88f881-b831-48a0-87ca-f9b967e91409 | hlm004-cp1-c1-m3-mgmt | True           | :-)   | active   |
+--------------------------------------+-----------------------+----------------+-------+----------+