I believe it would be a gift at the time when she put the proceeds from the sale of (her) house into (your) joint account. So if the amount was more than $14,000 per person (spouse involved?) then a gift tax return was due at that time.
Now, the money is yours. Whether the bank wants a gift letter now or wants to see it in a solely owned account is up to their underwriting department. Since the usually require documentation of the source of any large movements of money right before buying a house, my guess is you should leave the money in the joint account. If you move it, the bank might require a gift letter, but that's separate from the IRS.
