If you have a very large collection, it may be causing WA to exceed the memory a 32-bit app is allowed to allocate (in total or what works well on your system).
Scanning very large collections must be done in stages. Monitor WA's memory usage, if it gets too high stop the scanning and shutdown WA. Restart and resume the scanning, it picks up from where it was stopped. It may take several such stages to complete the scan of a large collection.
What is too much memory usage? That depends on your system resources and the OS you're using. A conservative number would be 600 MB, imo.
If it's not a memory issue, then maybe you're exceeding the path + filename characters limit (256).
Win 7 Home Premium 64-bit SP1, WA Pro 184.108.40.20692 beta, cPro MPxi_remix skin, 5.1 speaker system