Thanks for linking that thread, I went through and analysed all the hives in the config folder as well as the ntuser.dat hive using the Registry Explorer and SequenceNumberChecker tools.
I didn't find any issues with the Components, ELAM, SAM and NTUSER.DAT hives, but the DEFAULT, DRIVER, SECURITY, SOFTWARE and SYSTEM hives all prompted the "Primary and secondary sequence numbers do not match" error. The DEFAULT hive also produced warnings: "Hbin header incorrect at absolute offset “0x1DE000”!!! Percent done: “82.99%”" and "Extra, non-zero data found beyond hive length! Check for erroneous data starting at “0x1DE000”!". The DRIVERS hive produced similar warnings but on top of them it also produced: "Hive length (“0x7B3000”) does not equal bytes read (“0x79A000”)!! Check the end of the hive for erroneous data"
I repaired the corrupted hives using the RegistryExplorer tool, copied them back into the config folder and booted into the effected OS, but the problem remained. I then tried repairing the hives using the SequenceNumberChecker tool, but this also did not fix my problem.
I did notice however, that when I analysed the repaired hives in the config folder after I had attempted to boot into their OS, the DEFAULT, SECURITY, SOFTWARE and SYSTEM (DRIVERS remained clean) had become corrupted again and produced the "Primary and secondary sequence numbers do not match" error. Is Windows corrupting the hives during the boot process?
