Are you running on a laptop? This is a common problem with switchable graphics - the game runs fine when it selects the Nvidia/ATI card, but when it selects the Intel card it has problems (usually due to old drivers, and any Intel drivers from before 2012 have........ problems)

As for the game not respecting the config, I'd make sure you're editing the Trove.cfg contained in %appdata%\Trove\Trove.cfg.

With regards to the DirectX slowdown, I fixed a bug earlier this week with vsync (vsync's currently always on in DirectX), so when the next patch goes out next week look for DirectX performance to improve.