Did your high-tech aircraft only have one HSI?/Magnetic Heading Reference System????
If your ADI differed from your Standby Attitude Indicator and there were no warning flags, I'd look for a third attitude reference for comparison. Similarly, I'd do the same with heading instruments.
Having said that, on the ground, under the influence of magnetic interference from terminal buildings, blast fences, etc, it is common to see large discrepancies between two remote compass systems (enough to generate comparator warning flags). In the air, however, there is much less chance of interference, so I'd be comparing the two HSI's with the Standby Compass. If you only had one Magnetic Heading Refence System, then the call might be a little harder...
Despite it's simplicity, the Whiskey Compass is not without it's faults. It is susceptible to magnetic fields generated by aircraft electrical systems. During maintenance compass swings, we carry out tests with most aircraft electrical systems switched on... and again with most electrical systems switched off. I've seen variations between the two of up to 5 degrees. The flux gates of remote compasses, on the other hand, can be found at the wingtips, further away from many of the disturbing influences (HF antennae, nav/strobe light power supplies, etc, aside).
Similarly, a slaved compass is not without its faults. It is an electronic device and, as such, is susceptible to failure. However, it should have fault detection circuits and will tell you if it has failed. As a MHR System may be integrated with your normal attitude gyros (for short term stabilization), I'd be checking to see that your respective attitude instruments were operating normally.
In your comparison between the two magnetic sensing devices, I'd be looking for any signs of stiction (stickyness) in the instruments. If possible, make a smooth turn in one direction, then return to your normal track, looking for any signs of jerkiness. The HSI compass card may not move smoothly, indicating a faulty mechanism within the instrument. Similarly, the ball in your whiskey compass may be binding (check that there are no bubbles in the liquid interfering with the movement). Not very scientific, but you could try, very gently, tapping the case, to see if that frees up the stickiness, allowing the compass to settle on the correct heading.
Without looking at the larger picture/knowing all the details it would be difficult to make a call either way, but hopefully this is of some help.
Regards.
Q.