I ended up doing a quick fix myself. In fact, I don't know why it would rewrite the subdomain in the first place. Maybe you can incorporate this into trunk if you get a chance.
svn diff
Index: amazon_associate_filter.php
===================================================================
--- amazon_associate_filter.php (revision 185613)
+++ amazon_associate_filter.php (working copy)
@@ -34,8 +34,8 @@
$affiliate_code=get_option('amazon_associate_filter_id');
$content=preg_replace(
- '/http:\/\/[^>]*?amazon.([^\/]*)\/([^>]*?ASIN|gp\/product|exec\/obidos\/tg\/detail\/-|[^>]*?dp)\/([0-9a-zA-Z]{10})[a-zA-Z0-9#\/\*\-\?\&\%\=\,\._;]*/i',
- 'http://www.amazon.$1/dp/$3/?tag='.$affiliate_code,
+ '/http:\/\/([^>]*?amazon.)([^\/]*)\/([^>]*?ASIN|gp\/product|exec\/obidos\/tg\/detail\/-|[^>]*?dp)\/([0-9a-zA-Z]{10})[a-zA-Z0-9#\/\*\-\?\&\%\=\,\._;]*/i',
+ 'http://$1$2/dp/$4/?tag='.$affiliate_code,
$content
);
return $content;