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We study a quantum two-level system under the influence of two independent baths, i.e., a sub-Ohmic pure dephasing bath and an Ohmic or sub-Ohmic relaxational bath. We show that cooling such a system invariably polarizes one of the two baths. A polarized relaxational bath creates an effective asymmetry. This asymmetry can be suppressed by additional dephasing noise. This being less effective, the more dominant low frequencies are in the dephasing noise. A polarized dephasing bath generates a large shift in the coherent oscillation frequency of the two-level system. This frequency shift is little affected by additional relaxational noise nor by the frequency distribution of the dephasing noise itself. As our model reflects a typical situation for superconducting phase qubits, our findings can help optimize cooling protocols for future quantum electronic devices.