I have the same "flying" bug as Janaba. If I Relto out it's fine when I get back. My resolution is 1280x1024.
I also have no baskets in Gira. I started out with all three, but on linking back with my second set of fireflies, one of them was gone. I moved the one remaining at the second crossing and tried again. On linking back with the fireflies again, I had no baskets at all.
The only other problem I've had is an invisible shelf on most stairways that I have to jump over to get to the top.
I do want to comment that the graphics, and especially the sounds, seem superior to both MOULa and Minkata. Bravo!
EDIT: After deleting Gira and Kemo several times with no luck keeping the baskets, I found a workaround. After setting the three baskets, instead of taking the book link in Gira to Kemo, I linked to Relto, and from there to Kemo. When I got the fireflies and linked back to Gira, I only had one basket, but that's better than none. I was able to walk on the edge of the wall of the cave where the two baskets should have been, and made it without touching the water, so I was able to finish Gira.