This is most likely caused by a faulty (cheap, incorrectly implemented) host controller card. The driver is the same in the two software versions but the newer software uses overlapped (asynchronous) I/O to maximize the upload speed from the 1480A unit. Bad host controller cards do not correctly implement asynchronous I/O.
You can disable the asynchronous I/Os by changing the following setting in your AppSettings.xml file (resides in your installation directory):
<NumAsyncIos>10</NumAsyncIos>
Change to :
<NumAsyncIos>1</NumAsyncIos>
If this doesn't help, please change your host controller card. If it is built into your computer then try another computer.
You can also install the latest version without the asynchronous I/O method: http://www.internationaltestinstruments.com/Downloads/1480A_Pro_Ver_3.6.1.exe
If the above doesn't help you can roll back the versions one by one to see which version starts working (we'll assist with this at that point).