Using the handheld meter, a clean clear glass washed by hand in hot water so it has no dishwasher soap residue or anti water spotting films on it and either some known 0 TDS RO/DI or a jug of distilled water measure your TDS at several spots.
Start with the tap water, fill the glass, insert the meter and let it stabilize, write the reading down then triple rinse the glass and meter in 0 TDS water. Next disconnect the DI and test the TDS directly from the RO membrane OUT, fill the glass enough to immerse the meter, let it stabilize, write it down and triple rinse the meter and glass in RO/DI water. Finally sample the RO/DI directly from the DI OUT, let the reading stabilize, write it down and do a final triple rinse with 0 TDS water and put the meter away clean and capped and turn the glass upside down so it stays clean for next time.
If everything is working correctly you should see a 96-98% reduction in TDS between the tap and the RO and 0 TDS from the RO/DI. If this is the case then your storage is dirty but it could be as simple as you have stuck your hands in it or maybe dipped a bucket in it or it has not been sealed or capped with a snug lid. Once you dispose of or use the remaining water give the container a vinegar bath and start over.
Inline meters are not ATC temperature compensated so have built in issues unless your air and wate rtemperatures are exactly the same which is never. Is your handheld ATC compensated? Do you have 65 psi available at the RO/DI, dual membranes require this as a minimum. What is your water temperature? What is your exact measured waste ratio using a measuring cup and clock or water for exactly one minute from the waste then the treated lines?