Okay since most of your seconds are 1 sec over and most of your delays are close except for a few sporadic ones try this.
'Update' your pikatimer. Now your delays are more accurate right but you're getting in to your game too late? Add one second to your calibrated time now. You're basically telling pikatimer, you're not giving enough time to get that initial delay. (EDITED: I was right the first time =.=')
Basically pikatimer works like this:
Second timer = calibrated second + (delay - calibrated delay)/60
and then the first timer is to help you start the clock from the first minute...
You increase your calibrated second so that your 2nd timer is pushed longer and thus you start your second timer earlier. However you are keeping the same delay.
I believe this is the reason why your seconds are off because pikatimer only adjusts the second timer in order to help you hit your delay. Its intentions are, if you're not hitting your delay at *suppose 50.00 seconds, maybe you can hit it at 50.78 seconds*. Technically this works, but because your delay is so off, it's causing you to hit it at 51.10 seconds. This was all theoretical, but you get the picture.
For this run you can do this updating, but for future breeds/catches I seriously recommend you to try recalibrating. Most people don't really have to, but maybe you should.