With a feed TDS of about 1000 a permeate TDS of about 100 suggests only 90% average rejection. I'd expect better of a new membrane so I suspect there may be leakage around it. Check the O-rings in the system following the manufacturer's instructions.
If, OTOH, the surge in output TDS is related to a surge in feed TDS then, yes, you will have to accept the fact that you have real problem water. A solution, used in places in the world where they brew with sea or brackish water, is to use two RO systems in tandem. If each is only capable of average rejection of 95% (50 ppm out for 1000 ppm in) the pair will give better than 99% rejection (2.5 ppm out of the second system if the first has 1000 coming in). You will need to figure out some way to interconnect the two such that the pressure into the second is high enough to operate it.