Multiple Regression Repeated Measures with a continuous independent variable

#1
I have a complete within-subjects 2x2x5 designs, i.e. all 12 subjects I have have done the 20 combinations of conditions. My problem is that the 3rd IV here is continuous, but the 5 levels are not equally spaced. When I just look at data scatter plot, I can clearly see a linear trend of my data. However, under SPSS's GLM - Repeated Measures, the effect is no longer there, because my data are not compared at the right intervals, I think.

I'm interested in using multiple regression, but I have no idea how to deal with the repeated measures design for multiple regression. Can anyone help me out? Should I start learning SAS or R to get over this obstacle?

I've been reading online, and there's some talks about treating the continuous variable as a covariate. Is that the way to go?

Thanks so much for any help you could give.