Hello pjenness,
I can suggest to export markers to .xml file and them remove them from project, then align photos and save the project. Then you can import the markers back, reset camer alignment and do Align Selected Cameras operation via GUI or using Python from the Console pane:
PhotoScan.app.document.chunk.alignCameras()
If it doesn't work, you can send the proejct to us and we'll calculate the camera alignment in our internal version and send the project back to you.
The update with the fix will be release in a week or two.