I suspect that when this happens it is because of a “bad driver” elsewhere in your system that temporary hogs resources away from the firewire channel. I would try disabling Wi-Fi and any other non essential hardware to see if this resolves the issue.
The Y/S drivers are rock solid, but care must still be taken to make sure that there are no IRQ Conflicts elsewhere and that your PC / OS is set up configured correctly. BIOS settings (throttling/power settings) etc can also cause sound drop outs and just because old settings worked under a different sound card - (even if firewire connection previously used), this does not mean the same configuration will work on the MR816.
This issue has nothing to do with Cubase 5 version or bad MR drivers.
It is a case of unfortunately of thoroughly checking your PC system in all other areas to eliminate what is causing this. Make sure all drivers are up to date / no IRQ conflicts to rectify this issue /BIOS settings correctly configured e.g. CPU throttling/speedstep disabled.
I’m sorry that I can’t be more specific, but the MR816 works solid on my PC and thousands of other users, it is a superb piece of hardware. It should therefore theoretically also work on your PC setup when configured correctly.
Hope this helps…please do not lose patience.