What's wrong with my custom patch cables?

The other answers hinted at this, but I'm going to underscore it:

Pins 4 & 5 (the centermost two pins) must be on the same twisted pair.

Pins 3 & 6 (the pins just outside of 4 & 5) must be on the same twisted pair.

If you wired it "straight-through" as you said, without knowing about the special pairing requirements, then you probably did your pairs like this: (1 & 2), (3 & 4), (5 & 6), (7 & 8). That just won't work. You would've got pins 1, 2, 7, and 8 right, but pins 3, 4, 5, and 6 would be wrong. (I'll spare you the details of balanced-line transmission and noise cancellation.)

So follow the TIA/EIA-568-B standard as rob mentioned. Not only will it get the pairings right, but it'll make it easier when you or someone else has to work on those cables again.

One other thought: Inside the RJ-45 plugs, you know the little teeth that pierce through the insulation of the individual wires? The design of those teeth can be optimized for solid conductor wire, or optimized for stranded wire, or designed to work okay with either. If you happened to get the kind of RJ-45 plugs with teeth optimized for the opposite kind of wire from what you're using them on, they may not work reliably.