Network speed drops every other boot

Hi all, first post here. I have a weird problem on a computer I just built. It has a Gigabyte EP45-UD3R motherboard with built in gigabit network adapter. I have Cat5e cables running to a gigabit router to a D-Link DNS-323. I noticed I was getting slow transfer speeds so did a little investigating. I noticed that every other time the computer boots, it switches to 100 Mbps network speed (as displayed in the Task Manager Networking tab). The transfer speeds are consistent with 100Mbps. If I reboot, it goes back to 1Gbps and transfers at a normal speed (~18 MB/sec). I've swapped out with another machine and it consistently works at 1Gbps, so I'm assuming the cables and such are OK. I've gone into the device manager and set the network speed from Auto Negotiate to 1Gbps full duplex, but it doesn't help. Right now the task manager is showing 100Mbps while the network properties (Advanced tab) show 1Gbps. Any other settings I need to adjust? I've check the BIOS and didn't see any specific settings there besides enabling the network port.

Any help is much appreciated!