Each LED represents one of the front panel knobs - all the knobs except input level are represented. When you recall one of your previously stored user presets, it happens that the physical positions of the front knobs do not reflect what's going on inside the unit. This is also called an "override" situation - meaning that the software overrides the actual position of the knobs.
When an override situation happens with one of the knobs, the corresponding LED will light up to indicate this. The knob will not react to any adjustment during the override situation. To get out of this situation, twist the knob until the corresponding LED stops lighting - this means that you have now "caught" the parameter, and that your adjustments are taking effect.