I would say that at least in Windows (Win XP) this is "normal" thing for long time. Personally I ingest photos to one sub-directory, so main directory contains unchecked "daily" directories (/main_directory/yyyymmdd/). After I pick photos I will send them forward, I copy them to different directory (/main_directory/send/). If PM has this send directory as last used directory, I just press enter fast and it copies them right away. But if I wait, that PM starts to "read" whole tree, it takes those 10-20sec until it allows me to press enter to confirm destination.
PS: This main_directory is just for my unchecked photos, so it maybe contains 20-30 sub directories with about 5000 photos, but root of main directory is clean. On the other side, I have feeling it's working faster on Mac, but I'm running PM only on my Macbook Pro, where I normally don't have much more then 2 or 3 days old things.
And my info... 4.5.3 on WinXP, and 4.5.2 on Mac (will be upgrading as soon as I have some time
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