I have found that, for example, for AUDCAD there are some gaps in M1 SQX data that are not in raw M1 dukascopy data, please see the differences in attached images, there are missing data at the beginning of 2006 and between 2006 and 2007. The same happens when either "Standard download - Dukascopy servers" or "Fast Download from StrategyQuant CDN" is selected.
Please check the data for all the instruments, maybe Dukascopy has updated its data and Strategyquant is only synchronizing the last data from Dukascopy.