The solution is in QueueAdapter.MergeAllJobs do "JobInfoQueue.Remove(nextJob);" before "_jobInfoManager.Merge(firstJob, nextJob);" (swap them).
The cause for the wrong behavior is that JobInfoManager.Merge set nextJob.InfFile to null (by calling DeleteInf), but JobInfoQueue.Remove expects InfFile to contain the real path. It is used as a key to remove from _jobFileSet. Null in the InfFile causes the real path hangs in _jobFileSet and prevents a job with the same path being added afterwards (in JobInfoQueue.Add).
If do "remove" before "merge" then "remove" will work on the real path in InfFile and everything seems to work.
I tested it by rebuilding "PDFCreator.ComImplementation.dll" and replacing it in the installation folder.
The same correction needs to be applied in QueueAdapter.MergeJobs too.
I am hopeful the solution will be in the release.