Cut each acorn squash into 6 slices and remove seeds.
Pour the stock and cider vinegar into a 6-quart slow cooker. Add the squash slices, drizzle with the olive oil, and sprinkle with the thyme leaves and some salt and pepper.
Cover and cook on high for 3 to 4 hours.
When the squash is fork-tender, heat a small saute pan over medium-high heat and add the butter. When hot but not smoking, add the thyme sprigs--they should sizzle--and fry for about 30 seconds, until darkened but not browned. Remove the sprigs to a paper towel-lined plate and let cool slightly before shaving off the leaves. Let the brown butter in the pan cool slightly, then drizzle it over the squash. Garnish with the fried thyme leaves.