I'll offer an opinion, although there a lot of possible variables here. My first thought is that the end mill is dull or damaged. When I see a cut go from smooth to rough like yours did, without any of the cutting conditions changing, then it says to me that the end mill is toast.
We don't know the grade of steel you're working with so guessing about cutting speeds is just that, a guess. However, most common bolts in grade 5 are something like 1030 or 1040 steel so a cutting speed somewhere between 60-220 sfm would work, depending on your depth of cut. Roughing end mills like to run a bit faster than finishing end mills so take the high end and say that a cutting speed of 220 would work. This gives you an rpm somewhere near 3000 rpm for a depth of cut of about 0.02-0.04". So, for a 1/4" cobalt roughing end mill taking a 0.02" deep cut, I would suggest you increase your speed. For most cutters, the proper speed is more important than feed speed where cutter life is concerned. Quite often, you can just feel or listen to the machine as it cuts and get close enough to the right feed to get the job done. Roughers like to feed faster than finishing end mills, by the way.
Insofar as cutter material is concerned, I have used HSS, Cobalt and Carbide roughers on my Sherline mill and RF-31 and have no issues. Even my Sherline mill will cut well with these tools as long as I get my cutting conditions right. I use carbide tools when I need accuracy and stiffness in a deep cut, deep meaning a depth of cut the full diameter of the cutter, but cobalt is my go-to material for most stuff.
So, I would switch to a sharp rougher and see what happens. On a surface cut like you're doing, a 3-4 flute 0.025" finishing end mill will work as well or better but slow the speed a bit, say 2200 - 2500 rpm. If you feed manually, listen to the machine and feel for a slight resistance to feed and the end mill should walk right through a shallow cut.
