So, I wanted to see if my two disk drives perform differently. However, the files produced are not the same. I ran an MD5 check on both of the two files and got different results. They were files ripped straight from the disk, encoded with FLAC, then decoded back to WAV. I do not think the problem is FLAC as that is what FLAC is made for - giving the same results. I think the rips are different from EAC. Is this a big deal? Does that mean they won't sound the same, though it may be indistinguishable?

no big deal.

that's due to the different drives' offest

If I were you I wouldn't brake my head about that matter. A track which wasn't accurately ripped doesn't implicitly have to contain audible flaws, e.g. crackling, hissing etc. Judging by AccurateRip one of my computer's drives tends to produce ripping errors as well, prior to becoming aware of that issue I had already ripped quite a bunch of CDs using it. This hasn't turned out being a serious problem so far, apart from only one exception I haven't stumbled across any rips which contain any audible errors yet. And this exception was quickly re-ripped using the other drive - no big deal.

Simply keep listening to your music as you've always done. If you became aware of audible distortions sometime, I'd suggest you to compare the copy to the source CD and rip it once more in case the distortion wasn't apparent in the source.

Jarn, first of all, you really don't have to make the check that complicated (CD > FLAC > WAV...). All you need to do is compare the value in the CRC column for each track on the two drives. These SHOULD be identical, IF...
If they are not I suggest you thoroughly review ALL relevant settings in EAC Options. You also must check the offset value for each drive. This value is different for each drive and you typically need a reference CD to set it right. If "binary-perfect" rip is what you're after you really need to read EAC documentation. Cheers!
Martin

I don't care about binary perfect, I just want all my audio data - so this doesn't necessarily mean I'm missing data, it could just be a different offset or something?

If both drives are working properly - and I see no reason to think they are not, then it is most likely error correction or offset.

If you want to know which one, follow blsof8bc's advice and set up the offset with a reference CD (which EAC will help you make). The info on how to do it is in the EAC documentation - it's easy to do.

Then run the comparison again, with and without error correction and see what you get.

If you don't care, then just keep listening and don't worry about it.

I've used up to 8 drives at a time - at least 4 different models across 2 manufacturers and two different machines - and once the offset's were set up correctly, they all produced identical rips, except with badly flawed disks.