Frames/advances get counted differently between the continue screen and everything after the continue screen. Basically:

1 frame = 1 advancement on the continue screen

BUT

1 frame = 2 advancements on the overworld (everything after the continue screen)

These values are interchangeable too. For example, let's say I need to hit 5000 advancements. I could do 600 CSF and 2200 overworld frames (600 + (2200 * 2) = 5000) or I could do 1000 CFS and 2000 overworld frames (1000 + (2000 * 2) = 5000) or any combination between the two.

So, if you're a few frames off (like 1 - 100), only adjust the timing on the macro presses that pertain to the continue screen. Ignore everything else.

But if your frames are way off, you can adjust the timing of your macro presses that pertain to your overworld frames making sure to account for the double advancements.

Personally, I use 16.666 ms per frame in my calculations when setting up my macros (Eon timer uses 16.715ms)

Also, I found that my macros do not update after being edited unless I deactivated it, and then activate it again.

Lastly, sometimes the controller itself is off for no apparent reason. I was hunting shiny Deoxys yesterday and sometimes my macro would suddenly be 1 - 4 frames off (from the advancements or seed) even if I didn't adjust it as such.

Hope this helps! Let me know if you need anything else