Can you post some pics of the area and the membrane that was installed? Rubber roofs don't leach water except through seams, penetrations and laps seams. The problem with trying to patch rubber roofing of this age is that it chalks as it ages and cleaning it to accept sealant is sometimes difficult at best.
The only way to elevate the area that is holding water is to correct this situation when the roof is replaced.
Also, how was the rubber installed, loose laid over the decking or fully adhered to the substrate (glued)?
Oh, one more thing
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