Why does my phone peg the CPU every time I wake it up?
Are you over/underclocking your CPU at all and/or using profiles?

A lot of users will underclock their CPU when the phone is sleeping, which may save battery. However, if you underclock too much (125 MHz), the phone will lag like crazy when it wakes. It is recommended to never underclock further than 250 MHz.

Aside from that, I'm not really sure anything would cause this to happen and would need more information to help you diagnose.