I can confirm this. I think it is a bug, and I will make the necessary bug report. Thanks for bringing this to our attention.
Here’s what I think is happening: Even if you use a different prefix, you can still use exp_something to access the table, EE will sort that out internally. I suspect that, upon detection that your db is using a different prefix, but you use exp in your query, it simply removes the leading “exp_” and replaces it with the “correct” prefix; which you were already using, though. So, if you’d use:
{exp:query limit="10" sql="SELECT poll_id FROM exp_eepoll"}
{/exp:query}
EE would automatically change that to
{exp:query limit="10" sql="SELECT poll_id FROM exp_cu_eepoll"}
{/exp:query}
which would be correct the first time around.