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I had a mysterious flat tire on my rear wheel after I had left the bike standing for the workday. I removed the wheel and changed the inner tube. I didn't think anything went wrong while doing that (e.g. I don't think I bumped the derailleur) but I did notice that the brake disc was rubbing slightly on the inner pad, so I adjusted the pad a tiny bit and it seemed to be fine. The disc wasn't visibly wobbling when I looked at it between the brake pads.

On the ride home, the chain was sometimes skipping on the rear sprockets and I had frequent trouble shifting. I suspect that the derailleur is misadjusted. Both the chain and rear cassette are pretty new, and I had no skipping problems before I changed the inner tube.

Before I try adjusting the derailleur, is there something else I should check? Is it possible that the quick-release skewer is too tight or loose causing the wheel to be misaligned?

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    Maybe you fix your wheel slightly slanted? If the sprocket angle is not straight, chains will keep skipping due to the angle. – mootmoot Jun 1 '16 at 16:20
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    Shifting problems can be caused by many things. Is your bike locked when at work? It almost sounds like the rear derailleur hanger could be bent. If you take it to your local bike shop they can easily tell with the proper tool. You can get an idea, though, but eye-balling it from the rear. Look to see if the idler gears line up with the chain and with the front derailleur. As @mootmoot suggested, you might just have gotten the wheel back on slightly cocked. You can check that by loosing the quick release with the bike sitting normally, then retighten it. Gravity helps ... – Lee-Man Jun 1 '16 at 16:28
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    It seems to have been something like that. I opened the quick release, reseated the wheel and retightened the quick release, and now the shifting is fine. The quick release was perhaps slightly easier to open than usual, so I tightened it by an extra quarter turn. I wonder if that can move the wheel sideways enough to affect shifting? – Jouni K. Seppänen Jun 1 '16 at 18:04
  • Is it possible someone put a boot into your bike while it was parked? – Criggie Jun 1 '16 at 21:48
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    You don't get a flat tyre everyday. The first show sign of wheel place out of angle, is your brakes. Cantilever-brakes are much easier to spot, you can easily spot the clearance different of brake shoes from both side. Disc brakes are much trickier to spot, disc rubbing slightly is the tell tale sign, but replacing a flat for disc brakes wheel always need slight adjustment on the brake disc. Please use method as suggest by @Lee-Man. – mootmoot Jun 2 '16 at 7:51
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Per your comments, looks like you just needed to re-seat the rear wheel. To be fair, I will say there are things you can do while changing a tire that may cause problems like this. But having to adjust the disc brake, then the shifting acting wrong is a dead giveaway that the wheel went back in a bit of a different angle than it came out.

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