Are two different tires marked with the same dimensions (700 x 25c) the same size? Both sets of tires are from different reputable manufactures but the details are the same. ie Clinchers folding etc. 

I recently changed my tires on a road bike, the clearance on top section of the rear seat stay was always very small with OEM wheels and tires. I would guess about 3-4mm. 

I got new tires with the same specs from different manufacture and at the recommended psi the clearance from the top of the seat stay is about 1mm and I never noticed it while riding about 3k miles. But once i took it apart i noticed that the tire has been rubbing on the seat stay. I can see the paint has rubbed of slightly. 

Update: picture below - hard to see because of brakes but the top of the seatstay is marked with red line and the top of the tire is marked with green line.


Wheels are true!
I'd check if the wheel was in properly and is in good condition (true) along with the tire being mounted properly on the rim.

There is some variation in tires true sizes despite being marked the same size, though half a cm would be a lot larger variation than one could reasonably expect, especially with older tires. Features like studs, knobs can also affect this. If you have reasonable clearance for a given size of tire, one should reasonably expect a similar tire from another manufacturer to also give reasonable clearance, though this is not always the case.