Well, Motion is a little...'Glitchy'. You either get used to it and find work arounds so you can take advantage of it's brilliant user interface, realtime playback and massive content library or save your pennies and shell out on AE, which, to be fair, is pretty rock solid.
For me, I've found that the only way to use Motion effectively is to learn the keyboard shortcuts, have NOTHING else running, and only one monitor. I have a similar setup to yours except mine is a Quad 3 and Motion is still extremely buggy. I have one 30" ACD, and now that I've learned the shortcuts for my most often used tasks (thank you Apple Pro Training Series book!) I can actually have iTunes, QuickTime, and FCP open as I work. However, I don't suggest having those apps open, knowing the keyboard short cuts have made it easier for me to doing things before the system boggs down and gets buggy.
Winston A. Cely
Editor/Owner | Della St. Media, LLC
Sound it out: Nu-clear, not nu-cu-lar.
Mac Pro 3GHz Dual-Core Intel Xeon
4 GB RAM | Final Cut Studio 5.1.4 | Aja Kona LHe