why don't you scrub your file? i have skyward sword, an it's only one file.(scrubbed). you must have every thing on the file for it to be split.( updates an all the other fillers they put on disc).
try scrubbing the file first then load it.
Good spot , I had Wii Backup Manager configured to keep everything rather than just the game partition, which is all I actually needed. Unfortunatly, having changed this I've still got a split ISO, with the wbf1 file being around 80Mb now and the total size showing as 4.08Mb. Not sure if your doing something different (different file manager/cluster size) but doesn't look like it will work for me and obviously won't work for games that are siginficantly larger in size.
I still think I'm missing something obvious as it would appear other people have no issues with split wbfs files going by earlier posts