Okay, this is a bit left field, but just in case…
The only time I had a serious problem with latency in Cubase was as a result of a (Steinberg) plugin, one of the compression plugins. There are settings that allow the compressor vst to run without big latency, but if these are not set you can get horrible latency that, irritatingly, is not measured anywhere by Cubase.
Are you running a project with Steinberg compression plugin?
Steve.