I’ve read back a little and I ‘think’ you had it set to Reference before running Audyssey but Audyssey told you the level was too high so you took it out of Reference and then run Audyssey again and all was ok. Then you switched it to Reference for watching movies but it wasn’t calibrated at that level. You may have introduced a 10db (guessing) boost. The reference setting isn’t a switch to turn on for movie watching and then turn off again.
Using a SPL meter can be a good guide for were the levels are so try to do this if you can. All speakers, including the sub, should be at the same level as a starting point. Then adjust the sub to suit afterwards.
Default settings are just that. They don’t know the circumstances of the room and certainly Reference Level defaults can often be too high for Audyssey calibration.