Your Nikon D60 has several settings that could result in inaccurate exposure.

• Exposure Compensation The D60 allows for up to +/- 5 stops of EC.
• Spot Metering This metering mode uses only about 2.5% of the center of the frame when metering. If that small part of your camera is pointed to a dark object when you meter it will result in overexposure.
• 3D Color Matrix II Metering Nikon's Matrix metering has come a long way from the early days when it was almost universally despised by most pros I knew who shot Nikon. But at the time the D60 was created it wasn't anywhere near the level it now is.

When you are in full Auto exposure mode the camera selects Matrix metering and disables Exposure Compensation. When you are in PSAM exposure modes the camera uses whatever metering mode and Exposure Compensation you have selected. Note that in Spot metering mode the camera meters the active focus point unless you have also selected Closest Subject for the setting under AF Area Mode in which case the camera meters the center of the frame.

It sounds like it may be possible that you have Spot metering selected along with AF Area Mode including the Closest Subject option and are unaware that the camera is not metering at the active AF point but is instead metering the center 2.5% of the frame. You may also have a good bit of positive Exposure Compensation selected.