This went on last year, and our team hasn't figured out what's going on yet. Sometimes (most of the time, it seems like) the code doesn't download to the robot. The dialog screen comes up, and then instantly disappears. The code on the robot hasn't changed. It's easy to tell if the code actually downloaded, because it takes much longer for the progress bar to load. And we can tell that it compiled (if we intentionally insert errors). We've tried this with code that printed to the screen as proof.

TL;DR: Sometimes the code doesn't download to the robot. This happens both when we are connected via Samantha and when we are connected via USB. This happens at the most inopportune moments and makes PID tuning impossible.

EDIT: Firmware version: 9.68. RobotC Version: 3.62. OS: 64-bit Windows 8.

Anyone? Or should I just deal with it?

You probably need to open a ticket with support@robotc.net.