ive seen many PFCs with highish knock counts that when Datalogged show low counts but with a single high count and as your hand controller stores the max count you wont really know where the problem is so make sure your tuner has datalogit.
An example would be a log that counts many times a second with a count of say 8-120-8-8-8 often with the high number only coming up the one time per run but your hand controller showing this high number making you think it realy has a constant knock,This could be one missed load site with to much timing etc or as often happens some mechanical noise.
Datalogit will pin point it allowing you to find a reason for it.
If the light keeps flashing then its not a one of knock.