Whats starting up with my windows?

Everytime windows starts up now I see 2 "pop ups" in the center of my screen, it's like a small 1x1 window, just pops up for less than a second and goes away. Makes me suspicious, how do I find out what that is?

That could be caused by a few things. If you recently went to install something new or an update it could be a short lived notice of something. The other possibily would be some type of adware being prevented from showing fully by your existing system protection(s).

The first often given advice is to run a security sweep of the entire system as a precaution as well as a good run of the Secunia Personal Software Inspector(PSI) to see if something needs your attention as far as software. It could be a simple alert to a newer version of something being available.

Examining the active processes by looking over everything with one of the free system information tools like Handle, SysMon, ProcMon, Process Explorer, etc. along with a good security sweep would be the first thought until it is known to be malware or software related. The PSI tool can help by alerting you to updates for all the programs you presently have on as far which ones have update pending.