Passing a PCI scan is only the tip of the iceberg. Keep in mind that there other requirements such as PA-DSS to meet. In the end it may be the merchant or bank that sets what software it will accept.
This is paraphrased from the https://www.pcisecuritystandards.org/ website:
When 7/1/2010 rolls around:
Acquirers must ensure their merchants, VNPs and agents use only PABP-compliant applications, which means that:
As of 7/1/2010, you must use PA-DSS certified e-commerce software on your web site.
As I stated above, there is a lot more to this issue than meets the eye.