The Plant Drug Analysis book: http://www.springer.com/us/book/9783642005732
has an excellent solvent system for quercetin. I believe if you follow its instructions exactly you will get a single spot for your new Sigma quercetin.
Hi, what is the purity of your quercetin standard? Have you evaluated the UV spectra of both spots? Are the spots pure? Does the new standard also shows 2 spots? For these I think you need to have TLC Densitometry. Kind regards