Trying to figure out what I'm not doing right here

I have just finished setting up TL-R600VPN router with a TL-SG108PE switch to manage my equipment and an EAP245 access point.

Everything is connected (hardwired) using Cat7 cabling throughout (threw out all the old Cat5e) 

If I plug my computer directly into the modem I'm getting between 400-500 Mbs service. This was also the speed I was getting using a gigabit hub in my office before rewiring. I was also getting this speed with the Cat7 cable as I had installed that prior to installing the TP-Link equipment.

However as soon as I started going through the router (i.e. PC connected directly to the router) the speed dropped to 110-140 mbs (didn't matter if I used Ports, 3, 4 or 5 - same on each)

I get the same speed if I go through the switch (although I haven't tried hooking the switch directly to the modem to see if I get the same performance problems)

Rate limiting is not turned on the router from what I can tell. Ping times are fine. I also saw a post earlier that ARP Spoofing can cause issues slowing down the router so I have that off as its not really something I need to worry about as much.

I've also checked to ensure everything is properly seated and all the equipment is plugged into a dedicated UPS to ensure smooth power flow to all the equipment in my 'communications room'.

Both the router and switch management are claiming that 1000 mbs is enabled on all ports.

Why would I not get at least the same speeds I was seeing before? My ISP should be the bottleneck, not the router.

Is there some other setting that needs to be enabled or disabled in order to get the full potential out of this device?