It sounds like you may have a filter enabled for that file upload in the settings. Check to make sure there is not an Image Manipulation setting enabled in your File Upload Preferences by accident.
Also, if you are only seeing this image on the frontend and not in the control panel, check to see if you are using CE Image or some other image manipulation code that is possibly changing the image display.
UPDATE: I suggest that you upgrade to ExpressionEngine v2.5.5 to eliminate a bug in your EE version as the issue. This seems very unique to your server setup and EE install so upgrading EE is the first step.