What is your sharpening routine? Just about every digital image needs sharpened, and generally, the required sharpening is different based on what you want to do with them. For instance, you would sharpen more for print than you would for sharing on the web. Also, depending on how you are resizing your photos, you may need to resharpen after they have been resized since you are throwing away data during the image resizing process.
Basically, each image needs to be sharpened and sharpened differently based on the subject, what you are going to do with it, and how large the image is. I'm not saying that is going to fix your focus issues, but it should at least let you know what is a focus issue and what is a sharpening issue.