Without seeing what your code was for your multilevel meta-analysis, I can't answer your question. However, in ordinary least-squares regression, including both PhaseSetting1 and PhaseSetting2 as indicator ("dummy") variables coded from the original dichotomous variable, Setting, in the way I described could have caused the problem you originally described, "Covariances constrained to the variance of the intercept", because of collinearity.
In multi-level analysis, the models at each level are usually considered distinct, though they are combined to allow the program (for example, PROC MIXED or PROC GLIMMIX) to estimate the parameters for these models. If an independent variable on one level were collinear with another independent variable on another level, I think that the collinearity would also show up; but, although plausible, I haven't checked whether this is true.