Hi
Actually, the problem is now solved.
It was question of delaying the PFL_RESET after S4 and MAXii start up, now it is perfect.
If somebody is interested, I can provide (much) more details.
Whilst doing so, I saw that the IP does something with the FLASH even when not in reset condition.
Unfortunately, this is not well documented and if somebody from ALTERA reads this tread, it would be nice to have a more consistent documentation on this PFL feature and some troubleshooting guidelines.
Timing diagrams of coarse, never can get enough of these.
Kind regards
Thomas