Weird speed issue

We have been trying to track down a weird speed issue at one of our locations. We have a 1Gb fiber circuit coming in and get the following speed results. Anyone have an idea on what might be causing it?

Router - Mikrotik CCR1009, no firewall or queues

Switch - Cisco 3560 10/100 with 1Gb uplinks

AP - Asus 5G, tested and works at other properties

Fiber--Router--AP, 800Mb down, 800Mb up

Fiber--Router--1Gb uplink to Switch--Laptop hardwired in 100Mb port, 95Mb down, 95Mb up

Fiber--Router--1Gb uplink to Switch--AP in 100Mb port, wireless 30Mb down, 95Mb up

Fiber--Router--100Mb uplink to Switch--Laptop hardwired in 100Mb port, 95Mb down, 95Mb up

Fiber--Router--100Mb uplink to Switch--AP in 100Mb port, wireless 95Mb down, 95Mb up

All speeds are expected except when we use a 1Gb uplink from the router to the switch. For some reason thats the only time we get 30Mb down. This has been tested multiple times with the same result. Even tried swapping to a different switch with the same results. Any ideas?