I think that might be the difference. Except for the coating and size I was thinking the end mills were the same but the 1/8" end mill has a very tight helix compared to the 3/8" one. Now that I look at the pictures it's obvious....
One thing is that the Niagara 3/8", 4-flute end mill you linked is a high-quality, well-known part. I am not surprised it cut well for you. I am not familiar at all with the carbide mill brand you linked, but the 1/8", 4-flute is not at all the same thing. The optimal speeds and feeds would be very different from those of the Niagara, not to mention I have no idea about the quality of the end mill, which could be a factor too.