I have a Hydra 2.7 with an FMII installation. Cold starting in the AM or after the car sits at work all day is pretty good. The problem I am running into is if the car is just shut off for a short period like an hour or so. It will crank and crank but not start. The injectors are ID1000's and I did not have this issue after installing them and changing the fuel table. It is just something that has gradually happened. Compression also looks good. I though it was flooding out but after pulling the plugs and inspecting them these is no evidence of excessive fuel.
I'm not as familiar as I would like to be with the tuning of the ECU. My guess is the cranking settings need tweaking. Over the entire range or just a particular temperature range?
What's up here?

 

I'm experiencing the same thing. By any chance, when it doesn't want to start does the battery drain from all the cranking? Or does it eventually start?

When this happens to me I need to get jumped. How often do you drive the car and how old is the battery? Also, what is your voltage target set to? You can find that in Tuning Maps>closed loop>target battery voltage (I think).

 

If it starts fine in the other regions, don't touch it. Just modify where you are having issues and blend it in a bit.