Might want to check your CPU temperatures, the new cooler might not be mounted properly causing overheating. Could also be a bad PCI-E riser. Your case does allow for installing your GPU without a riser and that is what I'd advise you to do, PCI-E risers can be a bit flaky and might not be worth the potential trouble if you don't absolutely have to use one due to case size restrictions. Since you have an aftermarket card that isn't an exhaust blower design, mounting your GPU vertically can actually be suboptimal for cooling as you have hot air blowing directly on the side panel of the case and back to your GPU.
If your CPU temperatures are okay, try running your card without the riser, if your problem goes away, then either leave your...