This happens on my phone too and it pisses me off. I selected it once while also having another theme selected and my iphone is nearly unusable. When it's on the lock screen, the HUD behind "Slide to Cancel" isn't smooth, it just appears in random locations. I've found that if you press the home button then immediately try to slide your finger on the phone, the screen tends to register the touch.
What pisses me off is I selected this Chipmunk theme once at work, it slowed my iphone waaaay down, and I had enough 'free time' to be persistent at getting to Winterboard (on page 2 for me) and ended up deselecting it and my phone was normal after a re-spring. So today I thought, let me try it again (don't know why, the Chipmunk is hilarious?) but I added Winterboard to the BossPrefs Dock and set BossPrefs to open on a double click of the home button, since the home button always registers when you click it for me. Well, BossPrefs tries to open, and even gets its home screen loaded and I see Winterboard on the dock, but then it crashes. And when Winterboard is on the BossPrefs dock, it's no longer on my springboard, period. I've resprung and restarted a bunch, no luck. I'm gonna try to SSH the files off my iphone and see what happens. If no luck there, I'll just restore the iphone and re-get all those apps...a pain, but not the end of the world...let you know how the SSH goes...