As far as I understand you, you have a RadSplitter with Orientation=Horizontal and two RadPanes in that splitter - top and bottom RadPanes (as you write about Height problems, otherwise, the panes will be as high as the splitter). The Height of the two RadPanes is different in FF and IE and the problem is that in IE, you get a scrollbar in your bottom RadPane.
If this is the case, the pane shows scrollbars most probably because of its content. As you do not mention what content you have placed in the problematic RadPane however, I cannot be sure. In case you could provide us with the code that demonstrates the problem, we will do our best to explain the different result and help you get the desired behavior.
Apart from this, you could try setting Scrolling=None for the bottom RadPane, that will hide its scrollbars, but in case you need those, the content will be cut off.
All the best,
the Telerik team