I'm not sure what you mean by "doesn't show up". Can you give an example for this device - stuff like this is device-dependent, so problems with a different device, using different recoveries and different ROMs, aren't necessarily relevant.
Conversely, have you confirmed that this tool works with the Desire? I ask because the Desire isn't on your device list, and for modifying system software I'd like to be certain that the method works for the device in question before recommending it.
The only case I've met where recovery can't install a ROM from SD is where it's an old zip using the older scripting and you have a more recent recovery which doesn't support that. That should only be an issue with the very earliest Desire ROMs (and if necessary there are older recoveries which can install those).