little late to post on this but ... read only flag? Wasn't aware of anything like that
anyway about mq2auth...
each computer you run mq2auth on adds two lines to MQ2Auth0.h, creating it if it does not exist. The method used doesn't matter, but the two lines from each computer must exist in the final MQ2Auth0.h,
at the time it is compiled into MQ2. The "final" MQ2Auth0.h must be in the MQ2Main directory.
If something were to be "corrupt", it would not "compile". So, the only things left are a) MQ2Auth0.h did not make its way back into MQ2Main directory (and you only compiled with the compiling computer's info!), b) The compile took place before MQ2Auth0.h was updated, c) Separate copies of MQ2Auth0.h were actually used...
Since you said 8 lines in the MQ2Auth0.h, my best guesses would be a and/or b.