Hi Chachii - huge thanks for the feedback.
About a week ago I redid all the 2D collision system, so all the 2D levels got changed - one of the main changes was the collision sorting for the player to the NPCs - so if you are in front of them, their sort layer gets bumped down, and when you are behind them, their sort layer gets bumped up so they are drawn in front of the player. Some of the flowers were still on a layer just one below the player, so when the NPCs get bumped down the sorting list, they get drawn below the flowers - I thought I'd got them all but must have missed a few.
I also redid the collisions to scenery - any specific objects where the sorting was bad? I'll go through the videos shortly - I'm currently re-writing the AI for the 3D FPS bits, so as soon as I've finished that I'll be going back to fix any issues with the main world/collisions.
Currently F2 saves - and it auto saves every time you play a video/game/arcade machine.
Thanks again for taking the time to play and comment and to do some videos - that is seriously awesome :)