The reason this happens is because of what is referred to as the "secure desktop". The secure desktop has actually been around ever since NT. Certain parts of the OS, such as the login screen, the Ctrl+Alt+Del screen, and the locked workstation screen are actually completely different desktop sessions from what you normally interact with. Programs cannot interact directly with the secure desktop — this is to prevent keyboard loggers, etc, from messing with secure areas.
In Windows Vista and later, UAC is also a secure desktop area. While it looks like just a dimmed desktop, what you are seeing is actually a different desktop space, with a darkened screenshot of whatever was on your screen. No other program can interact with the UAC secure desktop, so that a virus could not, for example, say yes to its own prompt. This applies to Synergy just as it applies to any other program — it simply is not allowed to interact with the UAC dimmed desktop.
If you want the full security benefits of UAC, you simply can't use synergy. But, if you need synergy, the best compromise would be to set UAC to still prompt, but not on the secure desktop. This will cause the UAC prompt to act as a normal window on the normal desktop, meaning synergy can access it.
Hopefully that helps. If it still doesn't work, I have a few more things I could add, but try that first and see if it's what you need.