Design inconsistency is a problem we all have to be aware of. By themselves, they can either range from low to high impact on your users. A global inconsistency can lead a user to a lowered perception of the sophistication of a website or a design team.
Another downfall to the inconsistency of a design element is that a user must take time to re-learn the layout of each individual new element variation. Although the complexity does not necessarily have to be large, it does prevent the design from allowing the user to be as efficient as they could be.
The recommendation is this. I may be a good idea in future releases of a design to ensure you complete one last pass over your design to check for the simple things: popup design, font treatment, image size/position treatments, and anything else you can think of that should be consistent. Through consistent usage of design elements, a user can leverage their existing understanding allowing them to become more efficient with your design and ultimately a higher opinion of your design teams capabilities.
Good Luck! ~e