I think I know what you mean.. like a gnawing kind of feeling, but not exactly nausea?

Are you considering seeing a doctor? Some things, like ulcers or reflux, can have symptoms like this.

Does it go away if you eat something? If this is strictly physical, I wonder if eating smaller, more frequent meals might help, or having a snack.

Or, maybe some meditation when it occurs would shed some light on what might be on your mind, but hidden from your conciousness. Possibly sitting quietly for a while (and doing breathing exercises, if you do that) would help bring up the thought/worry.

What do you think?