The Betfair website shows 'virtual prices' which they derive from cross-matching opportunities. Those virtual prices are not supplied to the API, hence the slight difference in the prices between the software and the website.
When you send a bet via the API it will still be matched by the exchange using virtual prices if there are any available (resulting in you getting a price improvement). So from a betting point of view, if you use API software then you are not missing out on the benefit of virtual prices.
I understand that virtual prices will be shown in the next generation of the Betfair API, but Betfair hasn't scheduled that for release until 2014.
Some other API software programs try to mimic the Betfair virtual prices, by using an algorithm to calculate and predict them. Cymatic software doesn't do that, it only shows genuine prices, not predicted virtual ones.
Regards,
Gavin