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That's weird... maybe send a report about that. To do that, open the console (key ~ or `) and type "report" (without quot. marks). Maybe also add some additional information (like "good fps but still runs bad" or something like that)... perhaps there is something else going on causing the stutter
Done.
I sincerely hope this is just some setting in the engine somewhere that got "bumped" on accident, because no other game I have "ignores" the FPS setting like this. And there's no way that this game, running at 1280x720 on this hardware with literally every special effect setting bottomed or turned off, is maxing at 60FPS and stuttering.