It could be as simple as you have a higher concentration of protein than you did before. At high concentration, some proteins tend to look yellow.

are you sure it's your protein, and not just another protein of similar mass? 10 mM is a very low concentration of imidazole for a His-tagged protein to elute at (I'm assuming you are using His tag). Is it contaminated by other proteins - this could make it brown. The only time I had bright yellow protein I was working with flavin binding proteins.

How (bright) yellow is it? Can you post a picture? Just out of curiosity.

There could be several reasons for brown color, but with yellow, it's really like only the flavoprotein.

What is that protein? Does it have any cofactor or anything?

You purified it already previously from the same cells using the same setup and got clear solution with activity, while this time it was yellow and no activity?

From your description it appears that the protein was purified then the purification fractions were stored for a period of time and then you noticed the yellow colour developing in the fractions that were originally clear, right?  If this is the case and your protein has tryptophanes then I've seen some industrial processes where sample storage has light exposure that induces photo degradation of the aromatic residues and produces a yellow color with very little change in the mass spec.  Also some UV detectors do not have the proper filter and the UV light will initiate photo oxidation to cause a yellow colour to eventually develop.  This couod also be the case for a contaminant in your preparation.  It is possible that air oxidation may do this to a contaminant as well.  

I am also confused by your sentence "it is recently eluting in low imidazole concentration".  Are you referring to the yellow sample or a new batch?

there are many proteins that can be purified using metal chelating chromatography without the addition of a HisTag at their N terminus. They would elute at very low concentrations as described. I would guess you are now purifying a contaminant that just happens to bind to the column. Or a degradation product of your original protein (without the hisTag).

I have only seen coloration of proteins after purification when they were concentrated in dialysis membranes using 'aquacide' or 'biorad concentrating resin'. In this case I suspect sulphurs from the membrane to be the culprit but have not proved it yet.

If it doesn't have the tag then it would elute at low Imidazole concentrations along with contaminants which may be yellow.  If chromogenic low molecular weight solutes are present then they could be binding to your protein or just free in solution.  You might do a wavelength scan versus absorbance of a tiny sample before and after dialysis with 6M guanidine to see if there' are small molecular weight chromogens that dialyze out.  The color may have nothing to do with activity but proper folding would be very relevant. Is there activity before the IMAC step?  Your protein may have to firstly be folded if there are cysteines present and I'm guessing there are at 64 kDa.  Does the purification require reducing conditions and if so then TCEP should be used for the Ni column to prevent Ni reduction. Do SDS-PAGE gels show purity?  If the mass was determined by LC/MS then the LC chromatogram could indicate the purity. What class of protein is this and I'm assuming it doesn't require post translational changes or oligomerization?  

If your protein has more number of tyrosine and tryptophan, it will show a tinch of yellow. Also if it is very high concentration, it would be added the color.

Do the protein known to have any cofactor or metal ions ??