Since the default biome id is no longer available, all BuildCraft configuration files from pre 5.0.0 are all broken. The variable name of BC biome ids has to be change to override all previous setups. See e.g. http://mod-buildcraft.com/forums/index.php?topic=3.0 for reports on the issue.

Workaround: delete the configuration file (.minecraft/config/buildcraft/main.conf) or edit it and change biome ids.

Would it not be better to detect invalid values and change them than to rename the properties? You run the risk of corrupting even worlds that aren't using invalid IDs.

The only scenario would be an old world that had by chance set the id to something out of the range of the new Minecraft ids.

Which is a fairly common scenario with all the biome mods around these days.

In any case, I have nothing against a fix for that purpose.