Only questions, no answers I'm afraid.
Do you premix the solvents, or rely on the pump?. What temperature is your column and lab solvents ( eg solvents brought in from stores and used before warming up )?. Are any of the solvent handling systems different ( polymeric, metal rather than glass )?. Did the column backpressure increase the same for good and bad batches, and was it increased when peak splitting occured. Does increasing the column temperature by 10C change the split peak behaviour of good or bad solvent?.
If your earlier methods worked fine, what were the sample solvents and mobile phase systems, and if they included THF, does using a bad batch also kill those analyses?. Were the sample concentrations the same?. Have you tried diluting the sample and injecting more?. If you perform multiple injections of blank sample solvent, after a couple of samples, then repeat those samples, is there any indication that the quantity of bad solvent will change the peak splitting onset.
Can you analyse the rubbish on the front of the columns - eg back flush then use nmr or MS. Was there any comment on the nature of the rubbish ( particulate, goo) ?. Is the rubbish soluble in a slightly more aggressive mobile phase, or if the pH is adjusted?.
The peroxide value of the "good" batch obviously has climbed, as it's exceeds the Merck spec ( 0.02 ), so it's hard to make any meaningful comparison, but I'd be asking Merck to check inventory for lots more

.
My recommendations would be to premix the mobile phase, allow it to stand for an hour and then filter. I'm dubious that it's the THF quality ( but it's possible ). I think something else is marginal, and you may have to modify your method systematically to find it. I'd start with sample solvent/concentration, mobile phase composition, and column temperature, as split peaks can often result from one of those.
Good luck
Bruce Hamilton