Yeah I think it is probably just fuel related settings. With petrol on 2200cc injectors your pulse widths are so small there is a very fine balance between getting enough fuel in to get it to fire or completely flooding it. With wasted spark you had a spark 1 revolution earlier so less chance of "flooding" it.
A couple of comments:
Your MAP sensor is reading wrong. Fixing this will mess up the rest of your tune however.
Pre-crank prime of 40ms is a ton for petrol with a 2200cc injector. 40ms is what my evo has for 550cc injectors so I would drop that to about 10ms.
The "first crank enrich" may be excessive, try that around 50%.
In regards to your comment about the injector timing - with large injectors like this you have poor atomisation, lots of liquid and less vapour, injecting later when the valve is open and there is the highest airflow in the port often does give an improvement in this scenario - especially as ethanol content increases. So if it does help with starting then I would ignore your tuner and give it what works best. You can add an extra column at 501RPM or whatever so that timing is only later during cranking if you need to. It is also more typical to advance injector timing at higher RPM so not too sure what the tuner is on about here.
Thanks Vaughan! I was able to lower my frequency by choose 2000ppm OC output on my Dakota Digital SGIG-5C which worked perfectly. I was ignorant to the frequency. Thanks to you posting that frequency I was able to figure out what to do.