This is because pikatimer aims for the exact target second instead of giving room for error. That's one of the annoyances I was fixing when I made mine.
This is also the reason why I began using Toast's timer as well.
On a side note, I just RNG'd a Timid hexflawless Suicune. Not only did I hit the seed in 5 minutes (third try), I also caught it in a Dive Ball without too much hassle (perhaps 10 Dive Balls until the capture).
Now, if only I could catch that Adamant/Jolly Ho-oh in a Luxury Ball. Of which, brings me to my question.
Is catch rate affected by the level of legends? Let's say I'm playing HG and Ho-oh is 45. Would it be any easier to catch him as 45 as opposed to him being 70 in SS?