First the version number of JMS is wrong because 1.2.2 does not exists.
perhaps you want to say 1.1.22 or 1.2.0 RC 2
The htaccess is a special file that is effectivelly present in the master website but may be copied or linked into the slave site.
So you have to check also the slave site definition and see how is defined the htaccess.
Does it exists in the deploy directory ?
Have you enabled the slave site global configuration with the apache mode rewrite and also the Joomla SEF.
I can tell you it works because your are using
www.jms2win.com that is a slave site of my company and that use the htaccess and Joomla SEF.
You have to check the htaccess of each slave site.