There could be many reasons for this. Maybe you don't have a weak root chakra, but astrological influences that have similar effects. Only you can know this.
Also, astrological influences can weaken one's chakra - but these influences are also commented to our past lives experiences (karma), so it's possible that these issues can great unfavorable astrological positions for one's base chakra.
Look at Saturn in your natal chart, having a debilitated or afflicted planet also influences the chakra corresponding to that planet being debilitated.