B737 Captain discovered enroute that he may have departed with less than required fuel on an ETOPS flight. There was a difference between flight plan fuel and release fuel apparently caused by glitches in new flight planning software.

Narrative

We departed with the required fuel on the release. At cruise our fuel calculations agreed with the FMC in that we had sufficient fuel to complete the flight. The fuel at landing was over 6000 LBS; which was above the minimum but less than usual for the ETOPS flights that we are used too. With the switch to the new flight planning software and fuel savings initiative with the company we thought that was just a new procedure. At the critical point we were within a 1000 LBS of the flight plan and continued. A turn around would have us landing with the same fuel at both ends of the flight plan. We also had sufficient fuel to continue just not the amount we were used too. I received an email from safety representatives for the airline indicating there was a problem with the software. The new fight planning software and the complexity of ETOPS fuel planning created a 'Perfect Storm' in which a shortage of required fuel could be masked without detection in the limited amount of time in a normal sequence of events in an ETOPS flight. I discussed the event with the First Officer and we both concluded that we had enough fuel but should have questioned the amount of fuel on the flight plan in more detail. In the future I will take more time to ensure the fuel requirements on the flight plan add up to equal the amount on the release.