I was getting the MCSF before I had the remap, although now it's getting worse (I didn't have a single MCSF for a few weeks after the remap) ... because I'm getting the MCSF on start up then I presume it is unlikely to be due to over boosting ... surely if it were due to overboosting I'd get it when out driving?
Chris, I had exactly the same symptoms on my 1.9JTD MCSF and safe mode before and after a remap, fine for a few months before and after the remap, and one day, beeep beeeep! Raaaage! It wouldn't happen on every journey, usually when overtaking on the motorway, accelerating up from low revs at seemingly random times.
Under warranty I had the turbo boost sensor, throttle body and EGR valve changed, a turbo strip-down and recon (the turbo recon made it far worse) over the space of about 9 months through the main dealer. The error codes wouldn't show anything conclusive, it was vague codes pointing to turbo boost sensor at +5V.
Took it to a local indie garage and they diagnosed it instantly as overboost, they said they've seen it all too often where it turns out there was a spike in the turbo pressure coming up for a fraction of a second but it was enough to trip the boost sensor out. Angel Tuning came back (they deserve a shout for being most excellent in their after sales service here) and tweaked the way the turbo comes in to bring it in from lower revs and slower, and managed to squeeze another horsepower or 2 out at the top end, bonus! Since they came back to tweak the map I've not had a peep out of the MCSF, that was about 9 months ago now.
Disclaimer: I can't say yours is the same problem as mine, different engine and all but it sounds similar and I could have saved myself 9 months of back and forth to the main dealer 25 miles away if I'd taken it to the indie 1/2 a mile round the corner. But I did get a load of new bits and a turbo recon, probably totalling thousands of pounds of work for free.