At this point, I think I have described everything I need in order to explain the current situation: all of the APTickets Cydia itself requested from Apple for iOS 6 are useless. The word "useless" is important, as it is not accurate to use the word "corrupt": the data that was uploaded was not lost or damaged, and in fact all of the tickets that were stored verified per the algorithm from MuscleNerd.
Instead, the requests being made via Cydia to collect SHSH information for iOS 6 did not result in useful tickets. This is because, in order to better emulate the requests Apple had been making when I first started the service, I filter the manifests I send to Apple to only include information about files that had the partial digests I discussed earlier, as only files that have partial digests are relevant for SHSH.
However, the APTicket signs complete digests, not partial digests, and so even descriptions of files that do not have partial digests need to be sent to TSS to get a complete ticket. What really should therefore be used as a filter is "files with digest information at all", not just those that have partial digests (there is never a partial digest without a full digest), effectively finding all "real" files.
The result is that the APTickets that were downloaded and saved by Cydia itself are not sufficient to boot a device. However, tickets that were downloaded or otherwise obtained by tools such as redsn0w, iFaith, or TinyUmbrella, will work fine. If those tickets are uploaded to Cydia and then downloaded back, they also will continue to work: it is only tickets downloaded by Cydia clients themselves that were affected.
