i had the same (or a related problem) and here is how I solved it.
I updated OSX from Tiger 10.4.x to Lion 10.7.4.
Analog Factory was v2.5.1 all the time, no updates in between
While copying around preset files between the folders Antoine mentioned, I experienced the same issues as some of you did: some folders did not exist, copied preferences are applied correctly but presets are still missing.
this is how it finally worked for me:
copy all *.prefs-files from
If folders do not exist, create them.
Don't miss the space in "Analog Factory" in the destination path!
On OSX, you may use the freeware tool EasyFind to search for files (since spotlight still hides some files)
Glad to have my presets back!