I only see two major differances with the showflat/showthreaded... (I'm using an old version of the importer, so it could be something else too lol)
1 - ShowFlat (see #import):
header("Location: {$URL}/ubbthreads.php{$var_start}ubb{$var_eq}showflat{$var_sep}Number{$var_eq}$old{$var_sep}site_id{$var_eq}$site_id#import");
1 - ShowThreaded:
header("Location: {$URL}/ubbthreads.php{$var_start}ubb{$var_eq}showthreaded{$var_sep}Number{$var_eq}$old{$var_sep}site_id{$var_eq}$site_id");
2 - ShowFlat:
header("Location: {$URL}/ubbthreads.php{$var_start}ubb{$var_eq}cfrm");
2 - ShowThreaded (see _sep vs _eq):
header("Location: {$URL}/ubbthreads.php{$var_start}ubb{$var_sep}cfrm");
Not sure, but you could try the #2 and make it be _eq vs _sep and see if it'd work...