Apologies, I find this a little bit a non-issue as it states clearly everywhere that WPML works 100% when you use a permalinks structure of day and name (http://domain.com/2012/02/07/sample-post/).
If this is something you cannot accept, then you’s better come to terms with the fact that WPML most likely is not going to work 100% for you.
Or, to answer your questions:
re 1. no, this has nothing to do with the fact that you use Hebrew words in your slugs
re 2. no, there are no other known issues related to WPEC and permalinks that you should be aware of
re 3. the solution is to use a permalinks structure of day and name (http://domain.com/2012/02/07/sample-post/).
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