Do you have the correct versions of New_UIs and the Patcher - 7.2.0 and 1.0.77.0? And did you enable the Independent Engine Controls patch as Sober explains?
http://www.subsim.com/radioroom/showthread.php?t=197960
And are you using the Enhanced SH5 UI?
If you've got three "Yes"s, it's above my MOS. Maybe someone farther up the food chain can help?