Tim this happens A LOT actually, to the point where I wanted to find out why. It turns out Allow External Access flag value isn't copied from your source company code during Copy but from whichever company code has ""Use as Default Company for Server Settings"".
Feel free to ask me other little known arcane details. E.g. When I worked for Sage I wrote up bug reports and once in a while it was because there were typos in the code. On one occasion I found it it was because the programmer's nails weren't cut (true story but they'll never cop to it)