I just read this thread and I would like to comment some information that have been discussed.
I already talked to Jim several time about the sampling of the first flux transition and the positioning of the index in regard with the current bit. As you probably know KryoFlux start sampling BEFORE the first index and stop sampling after the last index. This is the only way to get the correct value for the first flux. On top of that KF also provide the information about the position of the index inside the current flux. This allow to know exactly for the very first cell the “pre-index” time, the “post-index time”, as well as the correct length of the bit.
On the contrary SCP does not provide any information about the position of the index in regard to the current cell and it also provide a truncated value for the first cell. What is happening is that for the first flux the length is computed from the index and not from the beginning of the cell. At the end of the track the last cell is correctly pushed to the next revolution and here you get the correct length for the first cell of the next revolution.
With this information, and assuming there is not too much jitter, between two revolutions you can compute the approximate length of the first cell of the first revolution, and the approximate position of the index in respect to the first cell: You must add the length of all the cell in the first revolution and you subtract this value from the index to index time, the result is the pre-index time (as the pre index is pushed to the next revolution) …
In most case the fact that the first value is incorrect and not knowing the position of the index is not so much important, but in case of a Non Flux Area positioned over the index it is pretty bad as explained here http://atari-forum.com/viewtopic.php?f=104&t=27364
Another problem (mentioned by Ijor) is that in “real life” the PLL is locked to the cells long before the index. Again with KF it is possible to lock the PLL emulation before the beginning of the track and unfortunately there is no way to do this with SCP.