Planar markers are useful in robotics and computer vision for mapping and localisation. Given a detected marker in an image, a frequent task is to estimate the 6DOF pose of the marker relative to the camera, which is an instance of planar pose estimation (PPE). Although there are mature techniques, PPE suffers from a fundamental ambiguity problem, in that there can be more than one plausible pose solutions for a PPE instance. Especially when localisation of the marker corners is noisy, it is often difficult to disambiguate the pose solutions based on reprojection error alone. Previous methods choose between the possible solutions using a heuristic criterion, or simply ignore ambiguous markers. We propose to resolve the ambiguities by examining the consistencies of a set of markers across multiple views. Our specific contributions include a novel rotation averaging formulation that incorporates long-range dependencies between possible marker orientation solutions that arise from PPE ambiguities. We analyse the combinatorial complexity of the problem, and develop a novel lifted algorithm to effectively resolve marker pose ambiguities, without discarding any marker observations. Results on real and synthetic data show that our method is able to handle highly ambiguous inputs, and provides more accurate and/or complete marker-based mapping and localisation.