Hello Amy, thank you for answer.
This motherboard has the embedded graphic card Maxtor and BIOS sees it. No another PCI video not presented.
If I use E3-1226 v3 (third generation), I see "Internal Graphics" in Advanced -> PCI configuration, so I am able to select between "Internal Graphic" or "Onboard Video"
When I insert E3-1265 v4, this item is lost from Advanced -> PCI configuration, and I have only "Onboard Video" from BIOS
Checking the specifications of your motherboard I noticed that the Intel® Xeon® Processor E3-1226 v3 is not fully compatible to your motherboard, here you can check the compatibility ARK | Intel® Server Board S1200V3RPM, just access the link and click on Compatible Products.
Just keep in mind that you will get graphics either from your dedicated graphics(external card) card or the graphics embedded to the motherboard through. The VGA port is the graphics output built in to the motherboard. Another thing I want to mention is that Internal Graphics and On board Video mean the same.
This motherboard has the embedded video Maxtor, and Bios has relevant item - "Onboard Video"
I don't have any question to E3-1226 V3 processor with his internal graphic Intel HD Graphics P4600. Bios has the item "Internal graphics" and I am able enable/disable it.
I don't understand, why Bios item "Internal graphics" is lost, when I am inserting E3-1265L V4 processor. It has internal video - Iris Pro Graphics P6300. This processor is compatible with this motherboard http://ark.intel.com/products/88041/Intel-Xeon-Processor-E3-1265L-v4-6M-Cache-2_30-GHz#@compatibility and C226 chip is compatible with this graphics. I don't use any dedicated graphics (external card) in my case.
May be E3-1265L V4 has broken internal graphics in my case? I do not have the ability to quickly change the processor or motherboard and check it.