Thanks, and thanks for being our customer on the PiDrive Compute Centre!
Thinking back through your description, you said 3Hz HDD LED flashing and my brain was thinking the reciprocal (every 3 seconds: 0.33Hz), which is why I was going down the path of system powering. 3x/sec is most likely drive formatting. When the software is installed, new partitions are set up and formatting is set up using ext4 "lazy init" mode. This establishes enough formatting to mount the device and get going, but the rest of the formatting is done in the background after the partition is mounted. So when you launch Raspbian for the first time, the disk LED will start flashing. If Raspbian were the only OS installed, it would be installed with the partition expanded to fill the drive and in this case the background formatting would take quite a while on a 375GB drive (like 1/2 hour or more). If the system is powered off before the formatting is completed, it'll just start back up next time that OS/partition is launched. During the formatting process, the activity does impact system behavior and it's possible it could cause mouse response hesitation/funkiness. Does this sound like what you might possibly be observing? If so, can you try launching Raspbian PIXEL and let the system sit until the disk LED stops the 3Hz flashing, then recheck mouse response?
If you'd installed many/most of the OS install items during set-up, the Raspbian PIXEL partition would be smaller and the time to complete formatting would be shorter.
I just did a web search on ext4 lazy init and this thread describes it pretty well:
Let me know if this is on the right track.