Nessus Scan

[mikef () everfast com]

After a recent external PCI Compliant scan one of my web servers failed because the scanner determine that  "a port was 
open at the beginning of the scan, and is now closed...".  I've tried all sorts of things to get this corrected the 
results remain. I talked with our scanning vendor they don't seem to have answer as to how to correct the problem. When 
I do a Nessus Scan on the site, Nessus reports the issue as a security note and risk factor of '0', however the my PCI 
scanning vendor reports the problem as a risk factor of 4 thus causing the server to fail the scan and resulting a 
non-compliance report.

I haven't been able to find anything on how to address this issue. Where should i look to resolve this problem