Sub-nanoliter volumes of the Belousov-Zhabotinsky (BZ) reaction are sealed in microfluidic devices made from polydimethylsiloxane (PDMS). Bromine, which is a BZ reaction intermediate that participates in the inhibitory pathway of the reaction, is known to permeate into PDMS, and it has been suggested that PDMS and bromine can react (J. Phys. Chem. A. 108, 2004, 1325-1332). We characterize the extent to which PDMS affects BZ oscillations by varying the volume of the PDMS surrounding the BZ reactors. We measure how the oscillation period varies with PDMS volume and compare with a theoretical reaction-diffusion model, concluding that bromine reacts with PDMS. We demonstrate that minimizing the amount of PDMS by making the samples as thin as possible maximizes the number of oscillations before the BZ reaction reaches equilibrium and ceases to oscillate. We also demonstrate that the deleterious effects of the PDMS-BZ interactions are somewhat mitigated by imposing constant chemical boundary conditions through using a light-sensitive catalyst, ruthenium, in combination with patterned illumination. Furthermore, we show that light can modulate the frequency and phase of the BZ oscillators contained in a PDMS matrix by 20-30%.