First, put the card in long before you try to build. Also, going back to the main menu first, then going to build causes the firmware to re-read the table of contents on the card and thus the file should be there. Worst case, a press of the reset button after inserting the card is a good option to know the machine starts in a proper state.
On the computer side, I have had problems too. First, put the card in long before you try to build or write to it via rep-g. I've also seen it where the OS was accessing the card in another process and the card couldn't be written to. In older versions of rep-g this would cause rep-g to just crash and close. In that case, I remove the SD card, open rep-g, try again to write the file but because the card is removed, the location resorts to the local hard drive, then plug in the card and ensure it shows up in my computer and then attempt to write to it. The problem is rep-g is saving the path to the SD card between writes and when it's not available, it craps out.
Other options inlcude just writing the *s3g file to the deskop and manually drag and drop that file to the SD card.
