Just an update on the process... games downloaded to NTFS and md5's checked under windows, and the md5's are good.
Head's up.
Now under Ubuntu, I went to the drive I downloaded them to (backed them up under windows, just in case) and copied them to the Ubuntu Desktop. Ran Md5 sums...
joshupetersen@Seikatsu:~/Desktop$ md5sum Penumbra*.sh
d9ffa6de661af48044656e89fb2f0f33 PenumbraBlackPlague-2567.sh
b50f1b0b3b2ff6a0636204ba00ac959a PenumbraOverture-1.0.2553.sh
2d39d4b47bfec4c51da8410be7e4c574 PenumbraRequiem-2985.sh
Md5 sums had changed.
Now at this point, I went back to NTFS drive I copied them from, and, well, I'll just let you see the whole process...
[i]joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$[/i] [b]md5sum Penumbra*.sh[/b]
59a515f5d4800c607ef01c8e6d83eca9 PenumbraBlackPlague-2567.sh
20a9536807248e569664ddcd15b5e755 PenumbraOverture-1.0.2553.sh
d176d522ba39fb2fec6ba95175ca98d2 PenumbraRequiem-2985.sh
[i]joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$[/i] [b]sh PenumbraOverture-1.0.2553.sh[/b]
Verifying archive integrity...Error in MD5 checksums: a274f3714a84a095d18a5b4e76724fa3 is different from b935bf51819c941ba2da19ede79e157c
[i]joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$[/i] [b]md5sum Penumbra*.sh[/b]
59a515f5d4800c607ef01c8e6d83eca9 PenumbraBlackPlague-2567.sh
ed617a6ceb137d24fb8bca61d3f8e15e PenumbraOverture-1.0.2553.sh
e7fbd276e0eba83ee06e281e8b2dabe2 PenumbraRequiem-2985.sh
As you can see, before touching the files, (only reading them for copy), they were fine. But once I tried to sh them, they get frelled up. Not only that, but of the two not sh'd, one got screwed up, implying that the process of getting the md5 sum screwed it up, or the sh had an overflow issue. Either way, that's kind of a serious issues for ext4 to be causing.
Although I'm not happy about having to reinstall linux again, hopefully this can lead to some needed improvements in future of both what to plan for in the game designing for linux, and maybe something to get fixed in linux.
Anyway, thanks.
P.S.
Seeing Black Plague's md5sum unchanged, I tried again... here's my not-so-successful result:
joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$ md5 Penumbra*.sh
bash: md5: command not found
joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$ md5sum Penumbra*.sh
5674f7113dbcfa642bb19309ac7383dc PenumbraBlackPlague-2567.sh
ed617a6ceb137d24fb8bca61d3f8e15e PenumbraOverture-1.0.2553.sh
e7fbd276e0eba83ee06e281e8b2dabe2 PenumbraRequiem-2985.sh
joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$ md5sum Penumbra*.sh
5674f7113dbcfa642bb19309ac7383dc PenumbraBlackPlague-2567.sh
ed617a6ceb137d24fb8bca61d3f8e15e PenumbraOverture-1.0.2553.sh
e7fbd276e0eba83ee06e281e8b2dabe2 PenumbraRequiem-2985.sh
As you can see, md5summing again, didn't screw with the values, but shing did. Meaning that, likely, the problem is between sh and ext4, not with md5 and ext4, in case you're interested. (And maybe something for Frictional games to consider in future, .deb's are a bit more reliable than .sh's in installation ease, and the debian based linuxes are increasing in popularity.