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If you have owned this laptop for a while, it may be overheating. IF YOU ARE COMFORTABLE DOING SO, pop open the laptop, and clean out the heatsinks/dust filters/ everything. Otherwise, it could be a hard drive issue. For a laptop, I'm pretty sure that these cannot be replaced, so the whole...
Well, I can tell you that Minecraft, and indeed Java, are not exactly optimized. Minecraft is poorly coded, and java was not meant to run a game like Minecraft. Make sure to download the AMD driver for the r9 2xx, it probably was lost when you reinstalled windows.
-A fellow r9 290 owner.