Comparison to a folder was always considered more as a feature, then primary function. For a big part that is because such a check has to take much time.
To compare against a big document storage, we recommend using
PDAS (Plagiarism Detector Accumulator Server), that is specifically created to check against a database, containing thousands of documents, and does it much faster.
So it was a surprise to us, that some customers started using the Folder comparison in such a way, and we never really tested this feature with such big packs of files, nor we created it for the task.
I will definitely ask our RnD to have a look into it.
May I ask you for some info on the computer specifications, such as the CPU and amount of RAM your computer has? It can be helpful. Same as what number of documents are you trying to check against.