Discourse-annotated corpora are an important resource for the community, but they are often annotated according to different frameworks. This makes joint usage of the annotations difficult, preventing researchers from searching the corpora in a unified way, or using all annotated data jointly to train computational systems. Several theoretical proposals have recently been made for mapping the relational labels of different frameworks to each other, but these proposals have so far not been validated against existing annotations. The two largest discourse relation annotated resources, the Penn Discourse Treebank and the Rhetorical Structure Theory Discourse Treebank, have however been annotated on the same texts, allowing for a direct comparison of the annotation layers. We propose a method for automatically aligning the discourse segments, and then evaluate existing mapping proposals by comparing the empirically observed against the proposed mappings. Our analysis highlights the influence of segmentation on subsequent discourse relation labelling, and shows that while agreement between frameworks is reasonable for explicit relations, agreement on implicit relations is low. We identify several sources of systematic discrepancies between the two annotation schemes and discuss consequences for future annotation and for usage of the existing resources.