Forge 4.6.12.511 for Minecraft 1.4.6
My guess was, that the prefix on value or key names ("I:xxx", "S:xxx", "B:xxx" e.g.) is used to explicitly identift value types, and stand for integer, string, and boolean respectively.
Rummaging around in the global config file, I noticed that after I start the client for a second time (first time is when the global cfg is created), the version=3.3.0 (note the missing specifier) entry from /config/buildcraft/main.conf, will get turned into B:version=.
I'd reckon it should default to string instead, so it doesn't end in a parsing/casting error if you explicitly expect a value of the type specified.