If you just cut one end off a manufacture cable and then aligned the wires as you noted (brown, brown/white, green, green/white, blue, blue/white, orange, orange/white) you likely have a problem with the wire order.
There are two standards for cabling:
- T568A: green/white, green, orange/white, blue, blue/white, orange, brown/white, brown
- T568B: orange/white, orange, green/white, blue, blue/white, green, brown/white, brown
I would double check your manufactured end to ensure what the order is, and match that pattern on your re-terminated end.
As others mentioned, you can check your termination and cable with a cable tester. This should tell you if you have miss-wired or have a fault.
Also, if the cable you bought isn't using one of those standards... I wouldn't buy from them again.
Quick Edit
After seeing your comment, I realized that you transcribed the order you put them in, in reverse. Generally, you should read from the side without the clip from left to right.
Doing this would have read (orange/white orange, blue/white, blue, green/white, green, brown/white, brown). Compare to the T568B, and yes it's clear that your problem was with the wiring order.
Personally, because i have experience with them, I would use a Watchguard firewall, and setup a point to point VPN, its literally drag and drop creation in the system manager. The XTM-33W would work just fine, and are under $1k. http://www.watchguard.com/products/xtm-3/overview.asp
You would need a device on each end. This is assuming that your current switches are not capable of any type of advanced routing and could not simply be plugged in to each other with the existing cable. (or want to keep the networks physically separate.)
Best Answer
Since ethernet requires pins 1, 2, 3, and 6, I am assuming that the other end of the cable also has two heads. They have then used 4, 5, 7, 8 for a second run using the same cable. I'm not sure what you'll find on the other end of that cable, but, that is my guess as to what they did to save themselves from running two cables.
My guess is that there is another run somewhere on the switch that the run returns to so that you have a NAT box in your premise, and it runs back to their other switch that has a VLAN that is then connected to your network.