Join Date: Mar 2008
Location: The 'Wack, BC, Canada
Bikes: Norco (2), Miyata, Canondale, Soma, Redline
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The piece you took out is a spacer as the others have mentioned. The one you removed is just as important as the one you left in. They are typically used as a set to position the axle where the derrailleur wants it to sit while holding the axle square to the bike's center line. It sounds like you took the one side out and pushed the axle in further on that side. If so then your rear wheel is no longer in alignment with the center line of the bike. That may be why it feels funny now.
I hear you about the lack of contact area. And like griftereck I've seen a frame where the slot on the NDS is shorter than on the DS. Why they would do something like that defies logic. And if the setup has chewed at the frame from being pulled out a few times already then it becomes triply hard to ensure a good mounting. And it does look like they are barely into the slots. To get the best possible hold the inner flange nut and QR skewer should be in contact over the entire length of the slot edges. If not then I would say that something needs to be moved to make this the case. I wonder if someone in the past swapped out the quick release (QR) and the present QR isn't letting the wheel sit back far enough? Or perhaps the spacers are installed wrong and so the spacers aren't letting the axle sit back far enough? Or perhaps someone put in the wrong spacers at some point? It's often hard to determine stuff like this.
Then there's the issue that pulling the axle out of the dropouts may have damaged the metal to where there is no way to get a good hold even if you can shift it back a hair. In that case you don't have a lot of options, at least not cheap ones, but to move the axle position back to where the inner flange nut and QR can sit against undamaged metal for their entire contact surface. If that means removing the spacers to allow this shift either due to damage or to a badly set up original configuration then so be it. Note that the shifting may require some fixing up or may end up with some habits that you'll need to become acustomed to dealing with. But anything will be better than dealing with a wheel that is trying to leap away to freedom...
On the front fork I think griftereck hit the nail on the head again. I once had to file out and deepen the fork dropouts to allow a larger axle to fit correctly on a buildup using newer wheels. Without it the metal engagement of the QR and inner flange nuts looked really iffy. I carefully filed the slots until I saw I had a full surround contact for the QR and then I centered the wheel at the fork crown by touching up the "wide" side with a few short strokes of the file to trim the depth and center the wheel. It sounds like you may require that as well. If the dropouts don't stick down slightly past the QR edge and the edge of the axle flange nuts then it's time to mark the fork dropouts with a sharp pencil for some guide lines and start filing.