Yes, they are the same logo.
The original file (the .eps file) has CMYK colors which are used in print (where the support on which they`re printed is matte - paper).
The .jpg and the .pdf have RGB colors which are used on the web (where the monitor emits light from behind and makes them look brighter).
Maybe my explanation is weak dues to my poor english. You may find here a better explained article regarding the difference between CMYK and RGB.
http://marvin.mrtoads.com/rgb_vs_cmyk.htmlAll the best.