Ruby application can't find gem that is installed

I used Passenger (via Application Manager) to deploy Redmine on my server. It had been working for months, but then stopped working. In the error log, I'm seeing: Could not spawn process for application /home/username/redmine: The application encountered the following error: Could not find rake-13.0.3 in any of the sources (Bundler::GemNotFound)
Funny thing is, I do have Rake 13.0.3 installed. In the Application Manager, the "Ensure dependencies" check comes in OK. In the terminal, "bundle check" comes back with "The Gemfile's dependencies are satisfied" so I really don't see any reason why the application can't find it. Running "bundle update" does not report any problems either. I'm not familiar enough with these things to know what to do...seems like I need to tell Remine where to find the gem, but I don't know where that would be done. Does anyone have some constructive suggestions for solving this problem? I've got a major project on hold until I can get my bug tracker working again. --Roland