Confirmed on Natty:

Fetched 13.7 MB in 12s (1,106 kB/s)                                                                                                                                                              
W: Failed to fetch bzip2:/var/lib/apt/lists/partial/us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_main_binary-i386_Packages  Hash Sum mismatch

W: Failed to fetch bzip2:/var/lib/apt/lists/partial/us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_universe_binary-i386_Packages  Hash Sum mismatch

W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com/ubuntu/dists/natty-updates/main/i18n/Index  No Hash entry in Release file /var/lib/apt/lists/partial/us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_main_i18n_Index

root@ip-10-117-77-162:/var/lib/apt/lists/partial# md5sum *
66b1e003087af95e4c3ecb2595888723  us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_main_binary-i386_Packages
 -- Matches universe/source/Sources.bz2
6c0170a630ab2c2526fce1a15a557cc7  us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_main_binary-i386_Packages.decomp.FAILED
 -- Matches universe/sources/Sources
27bb09fcfc7a4dee731a84d32ab59561  us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_main_i18n_Index
 -- Matches universe/binary-i386/Packages.bz2
5238567412ee16c16aa4dfb1282e4baa  us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_universe_binary-i386_Packages
 -- Matches main/binary-i386/Packages.bz2
57a2cf0d9cf10366d3905285f3507227  us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com_ubuntu_dists_natty-updates_universe_binary-i386_Packages.decomp.FAILED
 -- Matches main/binary-i386/Packages

From natty-updates Apt Sources:
 5238567412ee16c16aa4dfb1282e4baa           431291 main/binary-i386/Packages.bz2
 c757bc649fcb9fd50d9c5b895727daa8           554975 main/binary-i386/Packages.gz
 d7f12a4b835c3837b80f214b1dd6753e              102 main/binary-i386/Release
 57a2cf0d9cf10366d3905285f3507227          3333025 main/binary-i386/Packages
 f12dc36fa5dd364ae0b7776ba4bafa28           183259 universe/binary-i386/Packages.gz
 9f930c4d57ab8f70aab2d36f06a27b3d           779085 universe/binary-i386/Packages
 0951480c2c33548ec3618ab1082b77d9              106 universe/binary-i386/Release
 27bb09fcfc7a4dee731a84d32ab59561           138336 universe/binary-i386/Packages.bz2
 6c0170a630ab2c2526fce1a15a557cc7           149525 universe/source/Sources
 46cd339686c8e38c23a541190b436a29            46951 universe/source/Sources.gz
 66b1e003087af95e4c3ecb2595888723            40485 universe/source/Sources.bz2
 a4245d47dc44f65f4ce1786652c27c3d              108 universe/source/Release

And Curl headers:
root@ip-10-117-77-162:/var/lib/apt/lists/partial# curl -I http://us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com/ubuntu/dists/natty-updates/main/binary-i386/Packages.bz2
HTTP/1.1 200 OK
x-amz-id-2: HmP/KlL95l4732MGdCO2Yuz/Sx40eMJ0Z3XYspztQra8J9PjkNxajSKT/l4ZcQan
x-amz-request-id: CA9A66000053719F
Date: Tue, 06 Mar 2012 22:42:08 GMT
Last-Modified: Tue, 06 Mar 2012 20:56:01 GMT
ETag: "5238567412ee16c16aa4dfb1282e4baa"
Accept-Ranges: bytes
Content-Type: application/x-bzip2
Content-Length: 431291
Server: AmazonS3


root@ip-10-117-77-162:/var/lib/apt/lists/partial# curl -I http://us-east-1.ec2.archive.ubuntu.com.s3.amazonaws.com/ubuntu/dists/natty-updates/universe/binary-i386/Packages.bz2
HTTP/1.1 200 OK
x-amz-id-2: k5w77gQ/xKTUpSLSHnxrN6jAz0lCAsNT3HYcwZsJac1JNuntUUTwpJnnzle9rDI8
x-amz-request-id: E9CCB880DBF74437
Date: Tue, 06 Mar 2012 22:42:54 GMT
Last-Modified: Tue, 06 Mar 2012 08:52:52 GMT
ETag: "27bb09fcfc7a4dee731a84d32ab59561"
Accept-Ranges: bytes
Content-Type: application/x-bzip2
Content-Length: 138336
Server: AmazonS3