It's a known feature:
* In the very beginning, svn did not set the flag. Not even on the hidden .svn folder. So Windows indexed all files within the .svn folder as well.
* Then svn set the attribute on the .svn folder.
* then Windows started doing the indexing more aggressively, which resulted in svn failures during a checkout/update/whatever since the indexing service would open files for indexing and svn got 'access denied' errors for those files because the indexing server had them opened - so svn now sets the 'don't index' flag on all folders.
if you really want do have your source files indexed, you have to remove the flag manually.