I don't know anything about Synergy, but I have a guess as to what's going on.

In order for that UAC popup to be at all useful, they need to prevent most software from being able to ghost a click on the "Continue" button. If it were that simple, then a piece of malware could be written to do that, and get past UAC if a user accidentally runs it.

I'll bet Synergy falls into the "most software" category at the moment, and they'll need to upgrade it so that it can do whatever is necessary to get past that prompt. I'm not sure, from a third-party application standpoint, how that can be done. Perhaps it's a similar procedure as hooking into the GINA was (similar to what software like PC Anywhere had to do).

I know what you mean about trying to live with the popup. Mac OS X has a similar popup that I've learned to live with. The difference between living with the popup on the Mac, versus living with it in Vista, has two issues that get in my way:

1. All of the Mac software JUST WORKS whether the popup is there or not. Vista, on the other hand, has a few bits of software that won't work right unless I turn off UAC. You seem to have discovered one of your own just now. I have at least one MS internal tool that doesn't work with UAC.

2. On the Mac, if you want to just look at a control panel setting, you can do this without invoking the pop-up. Only when you want to change the setting do you need to supply administrator credentials. On Vista, simply opening the dialog box makes the popup appear, and you need credentials just to look at the setting.