So you're comparing apples with oranges now- the borehole SPTs have been performed at intervals through the profile; the CPTs are continuous. The sensitivity of the clays is a factor in the SPT interpretation.
Without any information on the size of the site, spread of the field tests, I can only assume that the borehole and CPTs were indeed put down through the same soil profile- if that's the case, almost certainly a question of the data interpretation...there is no ways your 3 to 5m of hard clay became soft from short-term storm-water mismanagement. A hard clay is effectively impermeable, at least in the short term.
An interesting point though- I've also observed some big disparities between SPTs and CPTs in sensitive clay soils...half the problem comes in relying on a printout with empirical values, instead of understanding the raw data. A SPT value of xxx doesn't necessarily mean a "hard" or a "soft" clay...it depends to a degree on the properties of the clay.
A final thought, in case the borehole was put down by a contractor of ill-repute...a badly worn SPT spoon can produce erroneous SPT values.
Best,
Mike