When Contextual variables are not set as expected, imported records by ImportHelper are created with System credentials (client 0, user 0 etc.)
Added patch to fix bug with missing context variables.
Thanks for comments, i am still learning how the community works Attached patch related only to this bug.
I found one bug related to this issue (it looks like it happens only when iDempiere is running from eclipse) which was already discussed in google groups:https://groups.google.com/forum/#!topic/idempiere/5YoY70HQXMg
Replication Processor overwrittes contextual variables of logged user, which leads to mentioned bug.
Attached additional patch to fix problem with global ctx variables.