Can you be a bit more descriptive? For instance, what are you purifying? Have you purified the same substance, and had a clear fraction (or different color)?
When I used to do a lot of purifications in the lab (with prep HPLC), I would get fractions of all different color tinges... which usually is the color of the component dissolved in the mobile phase.
When you dry your sample down to powder form, it is also yellow?