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As a first step, you may want to clear both your local browser, and java caches occasionally during the process.
Russ
If you are trying to replicate a folder structure have you tried using the "Upload Documents from Compressed File" action? It allows you to zip a folder structure (save path) and import the resulting zip into PDMLink/ProjectLink. The import process extracts the folder structure and documents from the zip file,replicating in PDMLink. The only drawback to this process is that you have to define one document type that applies to all documents in thezip (and similarly, can not independentlyset attribute values and description fields, etc.). But is sounds like a much more effective methodology than the one you are currently using (at least based on your description).
If you wantto be able to create more accurate information around the documents, then you should consider a bulk load or even a third-party tool that is purpose built for loading a lot of data (structured and unstructured) from a file system.
Steve