I had similar problems going from 4.08m to 4.09, although I wanted to keep my mods in place, so it might not be exactly the same issue.
I did as Caspar suggests, although I found that it was the file 'files.SFS' that was to blame.
Presumably I'm now missing some of the latest features, but it allowed me to install the planes, skins and maps from 4.09 and 4.10 without spending hours reinstalling in the correct order and then reinstall all my mods.
Inelegant solution, I know, but it's acceptible for me, since I don't play online.
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