Thanks for your report: apologies that PhotoStructure is misbehaving for you.
To remedy job queue issues, I made a bunch of improvements to job scheduling and concurrency management to v2.1, so I suspect the stable release of v2.1 will resolve your problem. Read more about it in this post. All the gory details are in the release notes.
Bug reports for alpha and beta (and stable) releases are always welcome! Please read this first before switching, though:
Alpha, beta, stable, and latest; What should you use?
That’s the plan!
As I add features, I typically add a setting or two (like I did with hide/delete/fave) that disable the feature, so if it’s not something you want, you’re in charge.