Clean URL/.htaccess problems with multiple subdirectories
It seems that your .htaccess is custom made, first of all you should have a look at the one Drupal provides as you're missing some criticals rules like 

&lt;FilesMatch "\.(engine|inc|info|install|make|module|profile|test|po|sh|.*sql|theme|tpl(\.php)?|xtmpl)$|^(\..*|Entries.*|Repository|Root|Tag|Template)$"&gt;
  Order allow,deny
&lt;/FilesMatch&gt;


Regarding your problem, I think you should change the RewriteBase condition like this:

RewriteBase /siteB_D6


for each of you subsite (make it matches the subdirectory where it's located).