Graph isomorphism problem for labeled graphs
You might be interested in this paper:

Aidan Hogan:
Skolemising Blank Nodes while Preserving Isomorphism. 
WWW 2015: 430-440

It has an algorithm (based on Nauty) for testing the isomorphism of RDF graphs, which are essentially directed labelled graphs that may contain fixed labels. The algorithm takes labels into account to narrow the search space.

If you can represent your input labelled graph as an RDF graph, you could try use the associated software package "blabel" to test isomorphism.