Hi Sarah,
You`re a lot sharper than some answerers ;) You are absolutely right that there is a virus/trojan that calls itself msiexec.exe - http://gsa.ca.com/virusinfo/virus.aspx?ID=43062
Malware can call itself anything it wants,so there may be others.
The one above comes in via AIM (aol instant messenger).It`s sent in a message with a link in it.
Of course that`s not to say your msiexec.exe is malware - it could just be the real msiexec playing up -but you should run a few antispyware programs,like Malwarebytes and Hitman Pro.
You might also check what other programs are running when the msiexec appears.
I`m thinking some program you installed recently is not quite installed properly.
Try and remember what program you installed recently.
Malwarebytes - http://www.bleepingcomputer.com/virus-removal/how-to-use-malwarebytes-anti-malware-tutorial
Hitman Pro - http://download.cnet.com/Hitman-Pro-3-32-bit/3000-2239_4-10895604.html
CCleaner (junk remover) - http://download.cnet.com/ccleaner/