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The d2x installer uses 2000# where # is the version of the cIOS. It's rather annoying. I just used ModMii to patch them to 65535 through Advanced downloads so they will still be recognized by SysCheck (using ShowMiiWads and the like doesn't work) and they won't get overwritten when I'm testing updates.I thought the cios installers learnt the "use version 65535 and it won't be overwritten" trick a long time ago.
I think that the 3.1 installer (or whichever one just came out) has an option to max out the version.