I just did this:
[ol][li]Added the Size(Bytes) column to the "Custom" folder format and verified that the column appeared in a new lister.[/li]
[li]Used the Import/Export wizard with just Preferences selected.[/li]
[li]Removed the Size(Bytes) column from the "Custom" format and verified that it no longer appeared in new listers.[/li]
[li]Used the Import/Export wizard to import the file I just exported, with just Preferences and, below it, Folder Path Formats selected.[/li][/ol]
Result: The Size(Bytes) column is back when I open new listers.
So it seems to work fine. Are you opening listers in the same way on the other machine? Is a Content Type format being activated there which stops the Custom format being reached? (More details on that kind of thing in the Folder Formats FAQ.)