Rear disc brake - clunky operation after winter

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Yesterday I took the bike out for a first ride this season. It sat in the garage since November of last year (temps always above 40F). It's a GT Transeo bike that I bought new last year. It's got Tektro Auriga Comp Hydraulic brakes.

When I apply the rear brake, I can feel it moving irregularly in a clunky sort of way, as if something was loose somewhere, but everything seems nice and tight. Can it be the brake pads inside the caliper that are loose? Sorry, this is my first bike with hydraulic brakes. What should I check?
 
Is it a dual piston caliper? If it were single piston I'd say the slider pins were gorked up somehow. Dual, well, maybe one piston is moving before the other. Might try making one stop from a cold start and immediately hitting both sides of the disc with an IR gun before it has a chance to conduct and even out the temps.
 
I would just do some inspection. Have someone repeatedly pull the brake lever and see if its getting hung up at all while extending out. I know on my Avid brakes the slides are fairly well exposed and its possible they just need some love. (lube)
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It sounds as if the pads are catching on the "vents" in the rotor.

Does this sound like it's possible? The pads should float fairly freely inside the calipers, they're usually held with a spring. I'd take the rear wheel off and check to make sure the springs are properly holding the pads.

Did you store the bike upside down or hanging vertically? A big "no-no" with hydraulic brake bikes. Some seem to fare okay, others not. Try squeezing the lever fairly hard a few times (not while riding, of course) and see if that might free them up.
 
Yes, it does sound like the pads are catching on the "vents" in the discs. I took the caliper off, took the pads out and inspected them. Everything looked perfectly fine. I put it all back together, yet the clunking noise and feel is still there when applying brakes rather firmly.

Squeezing the lever hard did not fix it either.

I did not store the bike upside down or hanging.
 
I'm not familiar with that specific brake and the mounting system they use, but as a starting point, take a look at the spacing between the pad and rotor on both sides and see if anything looks out of place. Is it possible something got moved over the winter and is now out of place?

The next step would obviously be aligning the caliper over the rotor so that it makes good contact with the rotor, simultaneously on both sides and is not angled oddly - such that one of the pads is toed in and is catching for that reason.
 
Nope, nothing's out of place.

I did align the caliper after the re-assembly. With these brakes, even the slightest misalignment would cause the pads to rub against the rotor, so it actually takes a while to get it just right.

Looks like I'm going to have to make a trip to the bike shop. I think it's still under warranty...
 
Meh... I rode all of about 5 miles and the clunk is back... looks like either the pads or the whole caliper cannot stay in place as it should...
 
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