Some users of FSXstarter told me, that they have problems after installing IvAP or UT2 because these programs did not work properly. For example IvAP adds the following line to your fsx.cfg:
[Edit 24.03.2014]: Use SIMstarter. SIMstarter uses Diff Manager to get aware of changes from other programs.
Please keep in mind: Every new config change made to fsx.cfg bei any other application or an installer will be overwritten by your FSXstarter profile. So far, that works as designed!