The times that I have run acovea, the benchmarks did vary widely in terms of the time required to run each benchmark, with some taking more than twice as long as the shortest test, so your experience does not seem totally out of whack to me.
However, it seems that if acovea is to give you good results, you really need to not have the computer do anything but run acovea. Earlier in this thread you can find my experience running acovea on my laptop from the command line, and another run where I was running a desktop environment at the same time. I got very different results between the two runs. It seems that for accurate results, you really cannot have anything else running at the same time.
For the most accurate results, I would recommend starting it on Friday night and finding something else to do for the weekend.
