Do not just measure the voltage across the gel box and divide by the box length. Temperature sensitivity is much larger than might be expected on the basis of simple thermodynamics because the properties of the DNA molecules are highly sensitive to temperature changes. Changes of 5-10 degrees C can affect running times by as much as a factor of 2. If the gel breaks at the loading wells, piece it back together on the scanner plate before taking the image. The image analysis software will fail if it cannot find the loading wells.
Dirt can cause serious problems for the image analysis if it is too severe.
We clean the gel plates with alconox, rinse thoroughly with deionized water, and dry them with isopropanol just before the gels are cast. We clean the scanner plate with alconox just before the stained gels are placed on top of it. Use a clean powder-free gloved hand to wipe the plates. Do not use KimWipes as they can leave residues. Make sure other glassware or plasticware used for agarose gels are clean.