Let me count the ways:
1. More than half the times the GUI does not even launch even though I get debug messages on the console.
2. Does not run on Windows 7 64 bit.
3. Does not run on Windows 7 32 bit.
4. Does not even run very well on any fast machines.
5. XP is the only machine it seems to like.
6. Even on slow machines when downloading large OS file (~25Meg) via USB it will hang and totally reboot the XP machine. (I have verified this on 3 different host machines).
7. The CDC version also is VERY, VERY slow to launch ... when it does launch.

Basically, It's gotten big and monstrous.

The underlying serial protocol isn't that complex, what adds up is the layering of TCL and support for a myriad of parts and external chips. Added to this is the attempts to evolve the tools, and provide some level of uniformity across some diverse parts that has changed over time.

It's not something I would remotely use in production. That needs a simple focused solution.

You may have a try with the latest SAM-BA 2.11.
It has been verified on WIN7 32/64-Bit platform.
It is true SAM-BA is only recommended for debug usage not manufacture.