I had exactly this problem after replacing the timing belt, intake manifold and EGR ....
and the answers NO i never did get to the bottom of it, after literally £0000's spent i got shot of her ... the alternate was a new engine or it was a cooked ECU.
I dont want to scare you but ... i had the same and replaced, egr, intake + actuator, throttle body, map sensor, maf sensor, fuel pump and injectors bosch tested, new fuel pressure sensor and fuel bar, leak back tested and injectors re-seated, timing checked about 3 times, replaced thermostat (shortly after this happened my cooling fans stopped working to) .... i came to the conclusion the ECU failed or had an error, plus it never had one fault on a full ECUSCAN check ... very strange !!!
I got shot of her !! never found it !!