You cannot create a kernel and a system file simultaneously so the timestamps are destined to be different. But which is newer? That is the question. The tools to create kernels vary fast with HP-UX, but with 11.11, here are some comments...

A copy of the system file used to create the kernel has been stored inside the kernel itself. To build a new kernel via the command line, HP suggests as a first step...
cd /stand/build
/usr/lbin/sysadm/system_prep -v -s system
This will suck the system file out of the kernel and deposit it /stand/build. The next step is to fiddle with some parameters with kmtune with -S /stand/build/system to use this particular system file. As you do, the system file changes and kmtune reports the changed value as "planned". It will become the real value if you proceed.

Unfortunately, HP then suggests you build the kernel via some steps that do not update /stand/system. Not a super big deal, since a new system file will be obtained to rebuild a kernel, but it leaves kmtune without a -S parameter a little bit in the dark. This is why I copy or move /stand/build/system to /stand/system as my last step in a kernel rebuild from the command line on 11.11. On the other hand, building a kernel via sam does update /stand/system correctly.

So this is why the confusion exists. Is your system file old and obsolete, or does it reflect your intentions for a change? Only you can say...