I guarantee you that the screws or standoffs did not change size.
First, look carefully at the screws you are using. The case will come with some intended for a different purpose and they will be slightly different.
Without the motherboard in place, test fit each screw to the standoff to be certain you have the correct one.
Next, when you mount the motherboard, do not tighten any of the screws until you have them all threaded. FWIW, I have found that a #2 magnetic tip Phillips head screwdriver is invaluable for tasks such as this.
A graphics card can be very heavy, and may slightly bend the motherboard. You may want to mount it after the motherboard is secured to the standoffs.