Sounds like it's set to overprint. Select your logo, make sure Window > Attributes is selected, and deselect 'Overprint Fill' / 'Overprint Stroke'.
Overprint basically leaves the background intact and prints your logo over it. If it's black, no problem, but white is generally seen as 'no ink'. If the background is printed, and no ink printed over it, you'll just see the background. If overprint is turned off, the white logo is knocked out of the background, making it visible again.
Hope this helps!