I copied all the files and folders under c:\Documents and Settings\[username]\Application Data\Thunderbird\Profiles\0c9iapp6.PJH\ to the folder k:\ThunderbirdPortable\App\DefaultData\profile\
All of the accounts appear but the subfolders do not.
Also, when I started a download from one account, it went back to Jan 24th.
My filters are not there.
My extensions are not there.
Have I misinterpreted what they meant when they said, "If you're using a local copy of Thunderbird, you may wish to just copy your local Thunderbird settings right into Thunderbird Portable. Your local Thunderbird profile is usually installed in C:\Documents and Settings\[user]\Application Data\Thunderbird\Profiles\default.???\ Just copy all of those files to the Data\profile directory within Thunderbird Portable."???