I'm still not sure why the boost and posix thread factories are missing, but the StdThreadFactory is working. For anyone that is interested, this is my config:
std::shared_ptr<apache::thrift::protocol::TProtocolFactory> protocolFactory(new apache::thrift::protocol::TBinaryProtocolFactory());
std::shared_ptr<apache::thrift::transport::TProcessor> processor(new cimnetservicerefactor::CIMNetServiceRefactorProcessor(stdHandler));
std::shared_ptr<apache::thrift::TProcessorFactory> processorFactory(new apache::thrift::TSingletonProcessorFactory(processor));
std::shared_ptr<apache::thrift::transport::TNonblockingServerTransport> serverTransport(new LocalhostOnlyServerSocket(port, machineName, localConnectionsOnly));
shared_ptr<apache::thrift::concurrency::StdThreadFactory> threadFactory = shared_ptr<apache::thrift::concurrency::StdThreadFactory>(new apache::thrift::concurrency::StdThreadFactory());
threadManager->threadFactory(threadFactory);
threadManager->start();
apache::thrift::server::TNonblockingServer server(processorFactory, protocolFactory, serverTransport, threadManager);