Sorry for the delay,
I did 5 non burst shots though i am not sure if these results are reliable as the value is normally 450-460, but after less than a second, it just changes to 500
I think what you are seeing is the value updating while the wait is happening, with the ISO just causing the UI to be refreshed to actually see it. The value is cleared when the raw hook is reached, and really shouldn't change outside of the actual wait.
The SD card used in the camera, is the PNY Elite Performance 64GB (read speeds are around 88MB/s and write speeds top out at about 60MB/s when used with a USB 3.0 card reader.
I wonder why the FP is lower with the script than with the manual single shot image?
This isn't about card speed. CHDK inserts code to capture the raw (the "raw hook") somewhere in some poorly understood Canon code. On some cameras, the Canon firmware hasn't always incremented the file counter by the time the code reaches this point. The "pause for file counter" setting makes the raw hook wait, either until the counter changes, or some timeout. The timeout is needed because the counter might be correct already. In that test build, the timeout is 500, so if FP is 500, it means the counter was already right.
I think what you are seeing is that in normal single shooting, the counter is right pretty much every time. So the code waits 500 ms (during which you can see the FP value change) and then continues. The wait is only consistently needed when shooting fast.
IIRC this matches results I got from someone else in IRC when the problem first came up for this camera.
We could make the pause longer in continuous mode, but that' wouldn't help scripts like this that just holds down shoot_half and clicks shoot full.
The current 1.3 (and 1.4) autobuilds will wait 320 ms, which was longer than any of your script results showed. This should fix the missing raw problem, but may slow down regular shooting, or the first shot in a burst.
Please let me know if you see the missing raw problem with 1.3.
I'll need to think more about other possible solutions or testing.