So I've been trying to fix this issue for a while now. So far, the games I've seen it affect are League of Legends, Duck Game, and Garry's Mod, but it doesn't affect Minecraft or Don't Starve when played fullscreen. The issue is a stutter in both video and audio in Garry's Mod, and it crashes LoL and Duck Game. I can play any game if I disable AMD CrossFire in CCC.
So before you suggest anything, I've tried clean installs of drivers, including any pre-existing ones on my system (the whole show of safe mode, removing all AMD software, etc.). I've also made sure that both of PCIe slots are working, as well as both cards, so no issues there. I then checked if the BIOS on the cards was an issue, and found that the R9 280 I purchased on eBay had a 280x BIOS flashed to it, so I flashed it to be the same as my current card, still to no avail. I've tried all the different combinations for the BIOS switches as well as CrossFire cable arrangement and swapping PCIe ports. I've double checked Windows 10 was up-to-date and that security was disabled through this process. I've tried factory settings for everything, and still, no results.
In AMD Crimson System Info, looking at the two cards, there are only two differences: 1) that one is in a PCI Express 2.0 x4 Bus Setting and the other is 3.0 x16 [which should make no difference since the motherboard is CrossFireX ready], and 2) the card in the top slot is labeled as AMD Radeon R9 200 Series #1 (Enabled) while the bottom card is AMD Radeon R9 200 Series #6 (Linked). Now I'm sure that the Enabled and Linked doesn't matter, but I'm not sure about the Series numbers. Yes, these were there numbers before flashing the new BIOS on the card.
Update while typing: The 2D Driver File Paths are also slightly different, though by one digit, being the last one.
Bottom card is:
2D Driver File Path
Top Card is:
2D Driver File Path
I am running an i7-3770, 4 sticks of 8GB Crucial Ballistix @1666, Kingston v300 SSD 240GB, 2 Hitachi 500GB 7200 RPM HDD in RAID 0, 2 Sapphire R9 280, and an EVGA Bronze 750w power supply. Any help is welcome if I haven't listed it already.