I am also experiencing this issue and would like an update as to whether it something that is likely to be addressed in a release sometime in the near future or if I should find a workaround to the issue.
My implementation is as follows, the autocomplete is starting out in a hidden div as per below
<div style="display: none">
<telerik:RadAutoCompleteBox runat="server" ID="autocomplete">
Then using jQuery I am picking it up and re-using it across a repeater so that I only need the overhead of having 1 autocompletebox on the page. Whilst I understand you probably don't support this type of thing with your controls I have quite successfully applied to same approach to comboboxes. Also If I se the div around the completebox to be initially visible this works a treat. Note that I have additional code that clears the completebox, loads the initial values into it then extracts them when done.
var picker = $find($telerik.$("div[id$=_autocomplete]").attr("id"));
var $picker = $telerik.$(picker.get_inputElement()).parents("div.RadAutoCompleteBox:first");