Highlight that capability prefixes are case-sensitive in the documentation: Configuring remote agent capabilities using Bamboo capabilities properties. The capability prefix should be in lowercase, for example:

system.builder.ant
system.builder.msbuild
system.builder.maven 

There's more information in this other page: List of default keys for the bamboo-capabilities.properties file:

Capability prefixes must be provided in lowercase format, while the capability name can use a combination of uppercase, lowercase and space characters.