Could you clarify the starting material a little more? Its a benzene ring with a phenol at 1 and 3, and an allyloxy at 5?
Perhaps you should do it at 0°C and add the MCPBA slowly. Formation of brown garbage smells of polymerization. Also, doing this under air and water free conditions if it isn't already is the first thing I do when a reaction is misbehaving.
My TLC shows complete disappearance of my product at only 1 hour but the mixture is still this awful looking dark brown.
Do you mean starting material disappears after 1 hr? if the product is showing up and then disappearing then I suspect polymerization even more. Poly-phenols like this have funny properties.
My hypothesis is that the phenols are attacking the epoxide intermolecularly via acid-catalyzed epoxide ring opening. The acid catalyst is coming from the benzoic acid byproduct.
One trick I do know though, is for workup, you should first do an aqueous sodium bisulfite wash to reduce the leftover MCPBA to its benzoic acid. Basic workups like aq bicarb don't do a good job of removing MCPBA, but do remove the benzoic acid derivative nicely. I fought this problem for a damn week before an older student dropped a knowledge bomb on me about it.