Uneven staining is almost always the result of insufficient agitation during staining.  The gel is initially more dense than the staining solution and will tend to sink to the bottom of the dish.  Some portions of the gel will have stains under them, others will not, and the gel will show darker and lighter areas as a result.

To recover this gel, simply continue the staining process with agitation (on a shaker), and the staining will become uniform.