It is also imperative that you make inquiries regarding the level of expertise and knowledge that the various agencies have about your particular industry. For example, if you are producing a food chemical such as citric acid or an amino acid, be sure that the Rabbi making the initial plant visit is familiar with industrial fermentations. Otherwise, his lack of understanding will almost certainly interfere with a smooth trouble-free certification. Likewise, Rabbis offering certification for dairies, beverage plants, bakeries, canning operations, etc. need to have a basic understanding of the technology and systems commonly used in each of these industries. Sometimes certain individual Rabbis erroneously prevent companies under their kosher certification from employing certain new procedures, or from using previously unapproved raw ingredients. Often this is due to their own inability to comprehend and determine that these new procedures do not affect the kosher status of the final product.
These are the types of pointed questions you should be asking to determine if the agency is really serious about servicing the companies it certifies. Ask the Rabbi for a list of all the companies under certification by this particular agency. Then, make some phone calls to determine if other companies have been satisfied with the level of service they have received.