Stock Pricing Calculations

I have seen on many occasions photographers websites that us a built in stock price calculator, such as with photoshelter or myloupe. This requires a potential buyer to input info such as size needed type of publication it will be used in (print, web ect..) circulation size publish frequency and so forth. My limited experience has been submitting to publications in return for a set price that is told up front by the publisher.
My question is, does having or using a stock agent and pricing guide that quotes a specific price have any effect on the price a publisher quotes to publish an image? The calculations I have seen with such tools have always been higher than any publications set price they offer. This seems to cause a conflict between what is quoted by the photographers site and the publishers proposal.
Thanks for your time.

Everything is negotiable within reason. Best to ask them first what they are interested in paying then counter with your own suggestion if you don't like that.

Richard's advice is the approach I always take. I ask what their budget allows for the use of my image and if we are close then we negotiate from there, if not then I thank them for their interest and say goodbye. Asking what they are budgeting has often resulted in my getting more than I was going to ask for.....of course, the opposite happens also.

Of course they want to pay less (if they can), but you're the seller of your photos. You set YOUR price. Do you walk into a store and tell them what you'll pay? No. This works for photographers and artists because, well... for lack of a better term... we're suckers. Of course, It's perfectly acceptable in many instances to take what a publisher offers, if you feel it's a fair fee. But if your shot is unique, special, or exactly what they are looking for, you should determine the value for yourself, and let them decide to buy or not, and not whether you should sell or not.

Hope that helps.