Brief freeze upon loading up from shut down

I may have selected the wrong section for this and if so, I appologize.
My system loads up after a reboot/shut down and then about 30 seconds or so after it loads up, will not respond to commands. This lasts for a few seconds and then everything I click during the *frozen period* happens all at once.
Mouse seems to be working/moving across screen, just what I asked it to do, it doesn't do.
I"m ttrying to track down what is going on during that time frame that causes this odd freeze (for want of a better word). Is there something out there for novices that might help me figure out what is bottlenecking my system upon startup?