Yeah, Third-party tools will often not display live rankings, which means that there could be a bit of a discrepancy between what the tool sees and what actually happens in Google. But at the same time I don't think you can totally rely on google tools by themselves either. There are some really useful features with 3rd party tools for competitor research, backlink tracking, keyword rank monitoring and just about anything else that google doesn't do.
So I think it's a good idea to use both Google and third-party programs for more analysis and information.