Wow - can't believe your issues are identical to the ones I've been facing for the past couple of months.
The only difference with my setup has been I was running pfsense virtualised (although now switched to bare metal for testing).
In particular, I thought I was going mad when I noticed whenever I woke a pc, the virgin connection would ping spike and I'd start getting packet loss. I tried all sorts of permutations to try and isolate the problem (I run quite a complex vlan setup at home), ending up with a very basic install to try and get to the bottom of the problem.
Only yesterday I noticed there are no ping spikes when running the SH3 in router mode, which then got me thinking it may be pfsense and/or a problem with virtualization and pfsense. So I've switched to bare metal pfsense now, and will report back findings. I suspect that factory resetting the hub yday may have had a positive impact? Is it possible they've tweaked the firmware quietly to resolve this issue?