It's been a while since I thought about my own setup, but I'm sure I have my particulate filter prior to the carbon filter??? I could be wrong there though!
Anywho....
With a 4040 your waste to pure ratio should be 50/50 if you are lucky, you can push it higher but the higher you push it the more you reduce the life of your membrane.
If you have it too high, your membrane will become clogged up and your production of pure water will increasingly slow down.
You may well have a knackered membrane, or a washer not seated correctly, but it won't hurt you to flush the membrane for a good 30 or 40 minutes, then reset the flow rate so that it is at BEST 50/50 pure to waste.
With my own 4040 I can fill my 1000l IBC tank in about 5 hours, and until recently the R/O was bringing my TDS reading down to around 0.004ppm which was absolutely fine for window cleaning....started to rise now though so have had to fit a DI vessel in the van.
You do need good mains pressure though, or a booster pump to get the best out of your 4040.
So try the above first before going to the - not inconsiderable - expense of buying a new membrane.
Ian