Yes, unless you’re using Google Analytics Premium, the Goal Flow Visualization will use sampling. That said, I’ve found the data discrepancies to be quite minor, well under 1% in most cases.

If your data is off by half, then I would first try narrowing your date range to see if that improves consistency. The longer the timeframe and more traffic you’re reporting on, the more larger that discrepancy may be. Second, as I noted above, be sure that you’re looking at identical criteria and are matching up the steps in your goals correctly. Given such a significant difference in your reporting, I would suspect that sampling isn’t the major issue.