Evidently, switching from ext4 to ext3 really doesn't make a difference, as evidenced by this:
On a reinstalled Ubuntu 9.04 i386
This is the files on the NTFS drive (restored from backup elsewhere on same drive)
joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$ md5sum Penumbra*.sh
59a515f5d4800c607ef01c8e6d83eca9 PenumbraBlackPlague-2567.sh
20a9536807248e569664ddcd15b5e755 PenumbraOverture-1.0.2553.sh
d176d522ba39fb2fec6ba95175ca98d2 PenumbraRequiem-2985.sh
Copy to Ubuntu side, then double-check
joshupetersen@Seikatsu:~/Desktop$ md5sum Penumbra*.sh
9553b54f63b38988301b6f404e9d88f7 PenumbraBlackPlague-2567.sh
5764c096fbcef3a910c701cc1676f8bd PenumbraOverture-1.0.2553.sh
cde17a58b11388572f952eb986b4b8db PenumbraRequiem-2985.sh
My response... Dang. I figured, oh well, try to run straight from NTFS folder....
joshupetersen@Seikatsu:/media/BigDrive/Ubuntu Downloads$ sh PenumbraOverture-1.0.2553.sh
Verifying archive integrity...Error in MD5 checksums: ea22c855950663eba8e0c1f90aebb23b is different from b935bf51819c941ba2da19ede79e157c
Frankly, at this point, I think I have a right to be slightly frustrated. Is there any possibility of getting these in a .deb format?