Answering my own question:
Kernel versions are different, but vanilla - 2.6.18-194.3.1.el5 on A,
2.6.18-92.1.10.el5 on B (but upgrading the kernel on B isn't possible right
now, neighter downgrading the kernel on A).
That proved to be the cause of the difference seen.
Yum does not update the modification time of the lock files when the old
kernel is installed, but does with the new kernel.
Issue (more or less) solved - thanks to everyone that might have bothered.
Thanks,
Iosif Fettich
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