If it i that you end up with duplication transactions. What and how are you importing, are these automatic downloads or manual downloads and imports, what file format are you using and what steps are you taking?
Always try to give as complete information as you can to aid in others helping.
For instance what version and build of MD and on what operating system?
I'm guessing by "quicken format" you mean QIF format although perhaps you mean QFX format in which case please ignore my comments.
What you describe would be expected behaviour if your QIF files contain entries that exist in other QIF files as the QIF format doesn't allow transaction identification. You will need to ensure your QIF files contain unique transactions - perhaps by setting date constraints when you download them. Alternatively, you could investigate downloading QFX/OFX format data instead as the OFX standard DOES allow for transaction identifies and MD will recognise and ignore previously imported transactions.