A 9 stop ND filter won't be exactly 9 stops, every filter manufacturer is slightly different, it could be anywhere between 8 and 10 stops!!! I would suggest that it is erring to the lower value since longer exposures were overexposed (or the light was changing see below)
The best way to sort out is:-
1) always shoot these type of shots a a certain aperture. I usually use f8, as this is typically in the lens sweetspot, and avoids getting any odd filter effects in focus!
2) Take a shot without filter, note exposure time eg 1/250 note the histogram
3) then take a series of shots with your 9 stop filter, check the histogram on each and hopefully you will have one that is close to the unfiltered shot.
Now you have a relationship between shutter speed and your filter
1/250 might be equivalent to 1.8 seconds with your 9 stop filter
then 1/125 = 3.6 seconds, 1/60 = 7.2 seconds, etc etc
Once your into really long exposures, you need to be adaptable as the light will be constantly changing, if it gets brighter, then you will have to shorten your exposure and vice versa. Its a bit of a black art, but practice makes it easier.
Hope that helps