Hmm... that's a dilly of a pickle.
I'm a Microsoft guy by trade, but will be making the switch to Mac when I'm done building my own studio (hopefully later this year). So, I'd be glad to help you out if I can. As you say, it works when you plug the two straight together, so it's gotta be in the cabling or punch downs somewhere.
Found a couple of interesting articles in the Mac support area, the least of which is that you may not have to even use a crossover cable. According to this:
http://support.apple.com/kb/HT2274 a Powerbook G4 or later has the ability to auto-detect the connection type and make the necessary "switch," so it shouldn't matter what type of cable you use. You were right to wire the wall plates as straight through tho.
Speaking of wiring- the punch downs will have two different standards you can follow- the "T568a" standard and the "T568b" standard. Do you know which one you followed? Hopefully, you followed the "a" standard which will be (from left to right) 1-green/white, 2-green, 3-orange/white, 4-blue, 5-blue/white, 6-orange, 7-brown/white, 8-brown. This is what a standard straight through cable will expect to connect to (at least, this is how my entire 100+ computer law office is wired. Seems to work really well). I'm not sure what the "b" standard is for, except to confuse everyone that uses the "a" standard.
So, to answer another couple of questions. From your post, you say it's about 100 ft from the house to the panel in the garage. By cat5e standards, you should be able to go 300ft without having to incorporate some type of repeater. So, big check mark on the length of run. Unless the cable was cheap and broke somewhere along the way when you pulled it, that piece should be fine.
Now, inside the studio. Again, length of run between machine room and control room shouldn't be an issue. You've done a great job at narrowing down the issue as you've already done the "do the computers see each other when plugged directly together" test. So, I'm pretty sure that the situation exists either in the cable or punch downs. "D'uh, I already told you that." I can tell you that the cabling company I use for the office sure wouldn't go out and spend a lot on buying the plugs for the wall plates, but that we have had issues where they didn't punch things down properly. They pulled the end off, re-punched it and voila problem solved. I'm assuming that there are no kinks in the run between rooms, right?
I'm also assuming you've got all the TCP/IP settings correct on both machines. I imagine if you didn't they wouldn't play well together when plugged directly together, right? Of course, if you look at that last sentence, and say "What the eff are you talking about Andy?" that may also be the issue.
Going back to my original idea, you could install a switch at the punch down (on the run from the house) and then plug each system into the switch. They would then get their TCP/IP settings from your router, should make them see each other reliably, and the switch would boost the signal and provide internet access to both systems. You wouldn't have to be changing the cable on the back of your studio system every time you wanted to go get some system updates or something. Looked it up at Future Shop, an 8port Cisco goes for less than $50 these days. If you can wait, they usually go on serious rebates in the next couple of weeks as the school year gets started.
Depending on how far up the road I am from you, I'd be glad to grab my testers etc and scoot down to help you if I can. Send me a PM and we'll work out the details if necessary.
Andy