That's strange, because BetterZip does not have any information about how it was started. Could it be that you have actually two copies of BetterZip in different folders on your hard disk and Finder uses each depending on the way you open the archive? After opening an archive, hold the Command key and click the BetterZip icon in the dock. This will reveal the location from which BetterZip was started. Is it really the same in both cases?