There should be no difference between the two. If the color model for two files is RGB, saving it in one format one the other should not produce color shifts - UNLESS - the jpg compression is so low that it's causing some of the colors to shift into the compressed palette.
As mentioned, the color model will be different in CMYK because a) a portion of grays and black are moved into the black channel, depending on gray component/under color removal settings, and b)there are colors in CMYK that will not display properly in RGB, and vice-versa. This is the most likely suspect.
I have noticed that some printers like to refer to "tif" and "CMYK" as synonymous, but they are not. A tiff can be RGB or CMYK, but so can a .jpg. Neither are exclusive.