MSI package generated by VS2008 will run custom actions under SYSTEM account. This "feature" was implemented to work around Vista's UAC.
There is no way to change this behavior from VS2008, but you can adjust MSI package using ORCA tool (available in SDK).
Start ORCA tool, open MSI package, navigate to custom actions. Select action which you would like to run under user account and subtract 0x800 from Type. In my case, value generated by VS2008 is 3090, new value should be 1042.
Save MSI back. Done