I feel so much better after today.
Was repeating a reaction from one of the postdocs (in order to assess reproducibility/set my own baseline). Took a TLC and lo and behold -- 8 spots. 3 above, 4 below my product, all chasing each other (but thank god they were at least resolved) Curse at TLC and crude for 5 minutes, go for lunch break/wallow in misery.
After lunch, decided to man up and run the damn column. Incorporated every piece of advice -- packed 10" column in hexanes, added toluene tracer and pushed in a good 5 cm, loaded in absolute minimum amount of DCM (~1 mL), flushed with 1 column volume of hexanes, pushed through another volume of 5% EtOAc/Hex, then finally eluted with 10% EtOAc/Hex (product runs ~0.15 in 10% EtOAc).
Product came out over 8 fractions, 1st fraction had some co-elution of upper spot. last fraction had some co-elution of lower spot, middle 6 clean. Pooled all 8 fractions, NMR sees barely any impurities (apart from residual solvent and a bit of grease).
So even with such a nightmarish TLC, I was still able to get relatively decent separation. Clearly I've been running all my columns wrong the past week.
I know this is an old post, but I'd just like to say that after reading this thread my separations have gotten a whole lot better. The tips mentioned here were really helpful - thanks!