Having read around a few forums on this, I thought I'd post my findings here in case anyone else goes for this combination with the expectation that it will work.
I have nearly completely given up trying to get my Harmony remote to work with my LC10M based MCE box. I'm quiite dissappointed. While the remote it clearly awsome, the thing that dissapointed me is the the Harmony website lets you specifically select the LC10M when you add a Media Centre device, but none of the buttons work. I can get some of the remote to work by just getting it to learn the iMon remote commands, but even with doing that, it doesn't seem to be able to correctly learn the Power On / Power Off toggle correctly.
I really like both the remote and the Silverstone LC10M box, but it seems pretty clear that they are not a good combination. if I want the Harmony to control everything nicely, I may have to buy an MCE remote and use its IR receiver rather than the LC10M's built in one.
Bummed
OK, here is an update.
I am approaching a workable outcome now, but to achieve this I have had to manually record all of the iMon IR signals for the Harmony. I'll be happy with it once I have it all going, but I think I shall remain dissapointed with the fact that the LC10M is one of the MCE choices for devices on the harmony website, yet that choice doesn't even come close to working.
