(Cleaning up old posts)
Custom metabase properties was not a well-used part of the product and was a big reason why IIS 7 has a rich configuration extensibility model with administrative tool support. So we avoid problems like you're seeing. I'd suggest using some alternative store for your settings such as an .INI file, or the registry (we used these for our URLScan module for it's custom configuration on IIS5 &6).
Dave