reposting question form yesterday
I ran into this problem a few times as well. At one point, I had a lower delay and higher seconds and visa versa. My "theory" was that it had to do with my calibrated delay being too high. However, I fixed it by just lowering/heightening my TARGET second when I'd hit a target second + 1 and target delay (making sure to do what ever delay adjustments I did before after entering the new number). After trying a few different combinations that way I was able to hit my desired times by telling PikaTimer that I was targeting 2 seconds earlier. *shrug*
Sorry for double post, but for the first time in my Smogon browsing history I saw a question I could possibly answer! Hope this helped.