rmaroney ,
Sorry that you are seeing this issue with MyEclipse.
Can you answer some more questions for us to understand the issue better ?
1) How did you upgrade to MyEclipse 9.1 ? Also share your OS and version details.
2) Can you switch to a new workspace in ME 9.1 , import the project and check if you still see the issue ? If yes then can you check the .log file which is located at <workspace dir>/.metadata/.log for any errors of interest and paste them here.
3) Can you also attach a screenshot of the error for us to help get a visual ?