I followed this procedure: (on a 250 gb original hard drive PS3 slim)
1. Deleted all unnecessary save files (had extremely many copies in some games like gow and ffxiii), game data files and games, amounting 30 gigs or so in total
2. Booted into recovery mode and ran rebuild database and restore filesystem
(I tried 2. without doing 1. earlier today without results.)
The pop in seems to have improved after this. It is still visible, but the objects that pop in are so small and far away that it feels acceptable. Additionally, and weirdly, it seems like anti-aliasing has improved along with the decreased pop in. (almost as if it was turned off before)