javascript problem with setTimeout

i have two frames in one page(in one frameset), the first one contains
a tree created by javascript and the other frame contains a text
field(contains refreshement iteration value)if i'm not working on the
tree(clicking it's nodes)the tree is refreshed and everything goes
well, but if i'm clicking the nodes and the refreshement time is due
nothing happens and it seems as if there is no refreshing at all and
the only triger to reactivate the refreshing is to enter the text field
and exit again, i don't know what is happening behind the scene, so can
anybody tell me what is happening and what is the apropriate soluation?
thanx