Without seeing the actual brushes, it is hard to give you an exact answer. Instead, I will briefly explain how brushes work in Photoshop (not sure about elements) in hopes that it will help you solve your problem.

Brushes are saved as shades of gray which represent the opacity levels. So even if your brush is set to 100% opacity, sections of it may still be transparent. The two circles in the image below are brushes that I defined. The solid black brush was used to draw the top two red lines and the gradient brush was used to draw the remaining lines. The opacity was set to 100%, yet the line drawn with the gradient brush are fairly transparent.

Brush Dynamics influence the result of dragging the brush tool across the canvas. Brushes have fixed dimensions but can be dragged an arbitrary length across the canvas. To deal with this fact, a copy of the brush is painted every so often. Brush dynamics control this process by specifies attributes like spacing (how often painting occurs). The red lines below all have different spacing which indirectly affects their transparency. There are many brush dynamics that can modified and they can produce some cool patterns; size jitter was used to draw the last red line.