That sucks. These are the worst problems when it works for some but not others. Teknoparrot can be a pain version to version. Only thing I could suggest would check your ParrotData.xml file and make sure you do indeed see <SilentMode>true</SilentMode>
I've been flipping between using multiple ways to start my Teknoparrot games (haven't decided on my favourite yet), but if you're so inclined, using RocketLauncher with it's loading screens always worked for me. It uses a more active window searching feature.
OMG, that game takes forever to load through Teknoparrot doesn't it. For games that have the option, (like Mario Kart DX), I try to use JConfig, as it loads faster.