What is a "semaphore timeout period?"
A semaphore (and a mutex) is a synchronization object, used to communicate amongst various processes sharing a resource. For example,if you had multiple threads performing division checks for primality, you would want to assign different divisors after each test finishes.
A thread needs to check the semaphore using a Wait Function to see if the object is free. However, to handle deadlocks should one thread fail to release a semaphore, wait functions can specify a finite time-out, the message you see. If a transfer takes too long, then the semaphore controlling it expires.
For more information, see WaitForSingleObject function, or the C++ Tutorial Multi-Threaded Programming.
So what might you do in a real-world situation when transferring large files over a network with limited bandwidth?
Compress the files (XML data, in particular, compresses ~10:1 with Zip).
Break the files into chunks (a nuisance, but applicable to any file type).
Improve bandwidth. For example, I found SSH/SFTP extremely slow on an older server, but when RAM was added, data transferred more rapidly.