Alright seems like we are getting somewhere. So my vita is an import from Japan but my account is Canadian, I think it should be downloading the U.S. version. However my md5 checksum isn't matching with yours so maybe it's actually getting the JP one? Still doesn't explain why it's not working in the converter.Not sure why it is failing. The sampling rate in the second screenshot is different from the first one you added so something is going wrong there. The first looks more consistant to a 16khz sampling rate which it should be. I'll post up the md5 checksum I have for the decrypted at9 file. If it differs from yours (I used the U.S. version of the theme) then that's where the problem might be I guess.
File: 20th_home_forVITA_re.at9
Size : 3.77 MB (3,960,360 bytes)
Size on disk : 3.77 MB (3,960,832 bytes)
CRC-32: 90d8e4da
MD4: 756ffa84dcce56614821cbccdfbd251f
MD5: 44193324e8b46ff0384ea3e3b0422d14
SHA-1: 341cbfe34727488aa07e7d5c7b5405e3bd60b0f8
20th_home_forVITA_re.at9
Size: 3,77 MB (3 960 360 bytes)
Size on disk: 3,77 MB (3 960 832 bytes)
CRC-32: dcf0c5bb
MD4: dd654fd4ab1439aee7c8c3bd39f1d95a
MD5: 0D4D75E95362ADC8E420A759DDBAD39E
SHA-1: 500a3e48b28066a9719e95ef4664593af05fd694