I see that now and then. It can depend on many factors.  How many other USB devices are drawing current?  How much?  For example, a USB powered hard drive? Are you plugged directly into the computer, or a monitor or keyboard?

Try a different port, often the front ports on a desktop aren't able to provide as much current.  Even laptops provide different amounts to different ports. 

When that happens, disconnect and then reconnect the Kindle to computer. It will now charge.

It charges fine from the wall adapter. When I plug it into my computer it says charging for a brief moment, then switches to saying it is not charging. transferring files works fine. It's a kindle 3 with 3G and screen savers hack. Is it a software issue?

Kindle doesn't charge from computer?