Hi Peter -
Please refresh us as to your setup/configuration. I have set up a number of M48 systems including both wasted spark, coil per plug and single coil/distributor and have not had the signals line-up. I try to arrange things so they do not coincide in order that the ECU detects an obvious sequence of events.
The cam sensor indicates to the ECU where TDC for Cyl 1 is, this it does from the Crip (Crank index position) value which represents the number of crank degrees between the Cam position signal and the Crank position signal.
As the cam rotates at half crank speed, this angular value can be up to 720 degrees. It is used to ensure that on a sequentially injected motor, the injector firing does so within a window of the valve opening. If incorrect, the motor will generally run, but the fuel will be spraying at a closed valve, sitting in the port until the valve opens and sucks the mixture in. On a V8 with individual coils per plug, it is important because it determines which coil fires and when. The coils fire in a sequence determined by hard wiring (M48) even though the firing order is entered into the ECU programming, it is only as a fault diagnosis aid. IF the crip is incorrect, the wrong cylinder's coil will fire dependant upon whether the crip is advanced or retarded. (pops and bangs or flames at inlet)...
On a 'distributor' install, it is still possible to have the motor run but with the injectors out of phase, the spark being 're-directed' by the lead placing on the dizzy. To check, you can set say a 5 degree ignition timing trim on one cyl - say '1' and then check to see that the strobe shows a retard on that spark lead, if it doesnt, strobe them all one by one till you find it and the crip error can be corrected by multiples of 90 degrees till it's correctly on cyl '1'.
Re sync errors - what do you actually get? I've not come across many systems that give ZERO errors, especially on start-up and even more so if (2-wire) magnetic type triggers are used. Speaking to Peter Knight of Knight Racing services (renowned UK motor builder/dyno), he too regularly see's sync errors on motors, especially those using MSD triggers, whether dizzy or crank (flying magnet) based.
Hope I've not 'muddied the waters' too much with this response...
Any chance of a few piccys?? a picture is worth a thousand words...