Other than selecting the shows for Transcoding / downloading, the client software doesn't have any role in the transcoding process. As noted in the software, you can turn off the client and return later to download.
However, there seems to be some recent problems with various HRs that prevent the transcode from starting. I know first hand that the HR24-500 has been on again / off again over the last year.
If it's a single HR on your network, reboot that HR and also do a 30 second reboot of GG.
While it shouldn't matter, you might try relocating the GG on your network. Avoid multiple switches.
I actually have mine on a DECA module and a 3' coax from a spliter on the wall with the SWiM-16. No problems with everybody other than the HR24.
I've found the best way to download multiple programs on the iPad is to make the selections from 'Ready to Download' and then start a program playing on the iPad. That keeps it from timing out and continues downloading.
There is no way to download via usb.