Hmm. Do you have back ups of all the data files from the broken installation?
It would be extremely helpful if we could determine exactly which data file was causing this problem
Even more specifically if we could determine what malformed or corrupt value/data resulted in this problem.
If you have a backup of the data files could you please install the portable edition into a custom location and test with the original data files, removing one by one until the problem is solved.
The files used by the Site Manager are cert.dat, bookmarks.dat, stats.dat, quick.dat, and sites.dat
I would test them in that order if possible.
I am still investigating this issue to determine what lead to this problem.
BTW you back easily backup/restore your whole ffxp config from within FlashFXP under the main menu > Tools > Backup/Restore Configuration
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