The acceleration of isolated neutral silicon cluster isomers in a helium gas expansion has been studied within a molecular beam experiment. The molecular beam flows through a nozzle tube that can be heated, expands into vacuum and the velocity slip of the clusters against the helium is investigated by a time-of-flight method. The measured mean cluster velocities can be analyzed by use of a simple acceleration model and give evidence for two structural classes of cluster isomers. Temperature depending investigations indicate that the cluster isomer class with an enhanced collision cross-section is metastable and transforms into the stable one if the nozzle tube is heated.