How big are the rasters?
You should probably try to run the Raster to polygon tool on a small subset to determine whether it's your tool or the size of the rasters. If the tool is still slow on the subset, then it's a problem with the tool. If it process the rasters perfectly you can probably set up a Python script that uses splits the raster up, converts to polygon, and then merges the polygonised raster back together.
Let me know if you need a hand with the scripting...