I agree with the sentiments previously expressed about multiple posts on the same subject.
But I do disagree (as usual) with Maxsteam about the validity, purpose and benefits of the shared ownership programs. They are a vital way to allow people onto the housing market where they may not normally be able to afford to. However, saying that, if the houseprices are massively overvalued then you have to wonder what value they offer if it is as expensive to buy a 50% share as it is to buy a 75% share of a property with 25% deposit.
I would do as Maxsteam has suggested and check out other similar house prices in the area, it may give you a bargaining tool. At the end of the day if a house is for sale there is almost certainly going to be some wiggle room in the asking price.
So far as the calculator. This could be your problem. The figures are not pie in the sky or figures to be aimed at but rigid set in stone figures that must be complied with. If you are faling short then this is most likely becuae your income is not sufficient for you to demonstrate affordability (within the associations tolerances) and as such to allow you to continue would mean they feel you could place your self in financial jeopardy to take on the purchase even though the bank may well have passed you for more. Don't forget that you will also be paying rent on portion of the house that you do not own and this will increase your costs.
It would still be worth having a chat with the company and see if there is anything you can include or exclude from your calculation that may benefit you but if all is correct and you still fail the calculator then you need to reassess and look at another property that is within your means as the shared equity association will not bend their rules to suit you