I hate to be a stick in the mud - but....
the Zune software on the PC really sucks.
it is sooooo veerrrryyyy slooooowww
it's so difficult to work with I find myself reverting back to using windows media player
(i still have issues with buffer overruns that sound like 'skips'. thought this was over with when we switched from analog to digital format music).
mp4's created on my windows phone playback with unacceptable lag
I think your problem is not the Zune software itself. It runs very fast. I have run it on a cheap netbook with no significant slowdown. On my main PC with a large music library it runs very smoothly.
What are your computer's specs?
Windows version?
Library size?
Where is your music stored? If it's stored on a network drive it will cause a dramatic speed decrease.
What kind of graphics adapter do you have and what visual settings are turned on in Zune?
Unless your computer is really slow I doubt the Zune software is to blame for the slowness. Though since Windows Media Player seems to work for you there may be some clash between Zune and your particular hardware or software.
If I were you I'd try a few basic troubleshooting steps: reinstall Zune, defragment your hard drive.