Inconsistency in results using IP filter (IIS Import)



I seem to be having an issue with piwik and the data it is showing. I am importing IIS logs using the file, the command I am executing is

python /usr/share/piwik/misc/log-analytics/ --url=http://xxxxx/piwik --idsite=1 --recorders=4 --show-progress-delay=30 --output=/xx/xx/analyse.log /xx/xxx/logs/u_ex*

I have created a segment within piwik which shows Visitor IP not equals … there are four of these which are linked with AND. We noticed that there were some inconsistencies with the data so I decided to create another site, import logs for the first 20 days of March but i specified within the settings to exclude the four IP addresses in the Websites Management.
For the site using the segment to filter we received 4363 visits, 309875 pageviews. Excluding the IPs with the website management we had 4553 views, 325419 pageviews. This is for same log files and the same period of time, so surely the results should be the same.

Could somebody please give me some guidance if I am importing the log files incorrectly or if this is the potential for a bug.