I am running Windows XP Professional as an administrator of the system, as I was for the other two computers, so permissions shouldn't be an issue but you never know these days... =p
My old desktop was more or less a basic backup computer in case of when my laptop was down (internet browsing, MS office use) and also acted as a NAS to my other computer. The new computer has software installed (in kind and amount) is similar to my main system, meaning a lot more loading at the beginning. Howeever this doesn't explain why my main computer is better off considering it loads more than the new computer does. All three have NOD32 as the resident virus scanner, though this new computer also has Malwarebytes and SuperAntiSpyware installed and loading at startup (turning those off from starting up at log in does not help.)
You say it loads settings from registry at 10%... you wouldn't think that would be too major of step, especially since the other older computers don't choke up there.
As for your comment about the age of your program, CS Fire Monitor is still a popular program for what it does, I could probably name at least a couple dozen people I have suggested the program to for its auditing/reporting functions, for the mini monitors and in a number of cases for cleanmem since its bundled with it, and that's just me. I'm sure other people that have downloaded it from CNET, MajorGeeks, etc have done what I have and essentially gloated about your program elswhere. =p That being said perhaps a second look at its code for optimizations, etc might be in order. =)
Well if push comes to shove I could revert back to version 2.5.5 and see if that helps, but I'm hoping that this will clear itself out, or that you have some suggestion.
edit: I reverted back to 2.5.5 and load time was maybe 2 seconds, no lag at all. What could version 3 be doing different?