I can't seem to reproduce you issues. You've piqued my curiousity. If you'd like me to test further here I'll need more information on how you prepare your source, including configuration files ("integrator.ini" from RVMi, "Last Session.ini" from nLite, and WinNT.sif). First I'll test the ISO in VirtualBox, then I'll try to troubleshoot any USB issues on my hardware.
For the record, v1.6 of the RyanVM Integrator was the first to support x64 sources. However, the "Optimize System Files" option was not altered to work correctly on x64 sources. I don't recommend using that option with any version of RVMi on x64 sources.
When the latest XPx64 update pack is applied alone the source will only lack updates for Internet Explorer. Slipstreaming a current IE addon will also slipstream the necessary IE updates into the source. Slipstreaming WMP11 will require you to also slipstream the current list of high priority updates to satisfy the Microsoft Update website. Other packages (like .NET) may have their own additional required updates.
Performed further tests myself with WinSetupFromUSB. I've found that, when all other variables are the same: FAT16, FAT32 and NTFS all work properly for me. Also, using NTFS on the USB drive provides a significant speed boost during Text-mode setup compared to either FAT alternative. Discovered that my standard nLite test configuration works properly (Last Session.J-2013-07-30.ini, same WinNT.sif and $OEM$ folder). Tried multiple sources on USB, too (XPx64 source posted above and an XPx86 with user_hidden's updatepack +drivers). And, while a bit off topic, my camera does not like NTFS or bootable SD cards.
