I'll explain this in too much detail, because it might be useful. When we import a flowjo workspace to create gates or compensation matrices, we also import the keywords that are cached in the workspace. We don't care about the actual FCS files at this point so we create fake run and fake fcsfiles to hang these attributes on.

The problem is that when we edit top-level analysis scripts we are showing these "fake" fcs files in the pane on the left, but we don't have proper file system paths for them. Any attempt to read the files in the gate editor causes a server exception at some point.

Since you have uploaded runs, you should see a drop down below the file list with the caption "Run". Choose different run, and I think the editor will work.

Let me know if this suggestion works.